Metadata-Version: 1.1
Name: pysam
-Version: 0.5
+Version: 0.6
Summary: pysam
Home-page: http://code.google.com/p/pysam/
Author: Andreas Heger
Metadata-Version: 1.1
Name: pysam
-Version: 0.5
+Version: 0.6
Summary: pysam
Home-page: http://code.google.com/p/pysam/
Author: Andreas Heger
pysam/TabProxies.c
pysam/TabProxies.pxd
pysam/TabProxies.pyx
-pysam/VCF.py
pysam/__init__.py
pysam/csamtools.c
pysam/csamtools.pxd
samtools/bam_import.c.pysam.c
samtools/bam_index.c.pysam.c
samtools/bam_lpileup.c.pysam.c
-samtools/bam_maqcns.c.pysam.c
-samtools/bam_maqcns.h
samtools/bam_mate.c.pysam.c
samtools/bam_md.c.pysam.c
samtools/bam_pileup.c.pysam.c
samtools/bam_plcmd.c.pysam.c
+samtools/bam_reheader.c.pysam.c
samtools/bam_rmdup.c.pysam.c
samtools/bam_rmdupse.c.pysam.c
samtools/bam_sort.c.pysam.c
samtools/errmod.h
samtools/faidx.c.pysam.c
samtools/faidx.h
-samtools/glf.c.pysam.c
-samtools/glf.h
samtools/kaln.c.pysam.c
samtools/kaln.h
samtools/khash.h
samtools/ksort.h
samtools/kstring.c.pysam.c
samtools/kstring.h
-samtools/msvc_compat.h
samtools/phase.c.pysam.c
samtools/pysam.h
samtools/razf.c.pysam.c
samtools/bcftools/kfunc.c.pysam.c
samtools/bcftools/kmin.c.pysam.c
samtools/bcftools/kmin.h
+samtools/bcftools/mut.c.pysam.c
samtools/bcftools/prob1.c.pysam.c
samtools/bcftools/prob1.h
samtools/bcftools/vcf.c.pysam.c
samtools/misc/md5.c.pysam.c
samtools/misc/md5.h
+samtools/misc/seqtk.c.pysam.c
samtools/win32/xcurses.h
samtools/win32/zconf.h
samtools/win32/zlib.h
tabix/ksort.h
tabix/kstring.c.pysam.c
tabix/kstring.h
-tabix/msvc_compat.h
tabix/pysam.h
tabix/tabix.h
tests/00README.txt
-/* Generated by Cython 0.13 on Thu May 5 14:57:52 2011 */
+/* Generated by Cython 0.14.1 on Thu Nov 17 22:34:01 2011 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#define PyBytes_Repr PyString_Repr
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
+#endif
+
+#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#endif
-
#ifndef PySet_CheckExact
-# define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
+ #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
+#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+
#if PY_MAJOR_VERSION >= 3
+ #define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
#define PyInt_Check(op) PyLong_Check(op)
#define PyInt_CheckExact(op) PyLong_CheckExact(op)
#endif
#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
+ #define PyBoolObject PyLongObject
#endif
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
#endif
+#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
+ #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
+ #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
+#else
+ #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
+ #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
+#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
#include "stdio.h"
#include "pythread.h"
+#ifdef PYREX_WITHOUT_ASSERTIONS
+#define CYTHON_WITHOUT_ASSERTIONS
+#endif
+
+
/* inline attribute */
#ifndef CYTHON_INLINE
#if defined(__GNUC__)
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
#define CYTHON_INLINE inline
#else
- #define CYTHON_INLINE
+ #define CYTHON_INLINE
#endif
#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
# endif
# elif defined(__ICC) || defined(__INTEL_COMPILER)
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
-# define CYTHON_UNUSED
+# define CYTHON_UNUSED
# endif
#endif
#ifdef __GNUC__
/* Test for GCC > 2.95 */
-#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
+#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
#define likely(x) __builtin_expect(!!(x), 1)
#define unlikely(x) __builtin_expect(!!(x), 0)
#else /* __GNUC__ > 2 ... */
static const char *__pyx_f[] = {
"TabProxies.pyx",
"bool.pxd",
+ "complex.pxd",
};
/* Type declarations */
-/* "pysam/TabProxies.pxd":42
+/* "TabProxies.pxd":42
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
int is_modified;
};
-/* "pysam/TabProxies.pxd":77
+/* "TabProxies.pxd":78
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
};
-/* "pysam/TabProxies.pxd":91
+/* "TabProxies.pxd":92
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
uint32_t pos;
};
-/* "pysam/TabProxies.pxd":60
+/* "TabProxies.pxd":61
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
int hasOwnAttributes;
};
-/* "pysam/TabProxies.pxd":80
+/* "TabProxies.pxd":81
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
};
-/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":20
+/* "TabProxies.pyx":20
* return not (buffer <= p < buffer + nbytes )
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
-/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":488
+/* "TabProxies.pyx":493
* self.fromDict( r )
*
* cdef class NamedTupleProxy( TupleProxy ): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
-/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":573
+/* "TabProxies.pyx":578
* TupleProxy._setindex(self, idx, str(value) )
*
* cdef class VCFProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
-/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":507
+/* "TabProxies.pyx":512
* return f( self.fields[idx] )
*
* cdef class BedProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
-/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":231
+/* "TabProxies.pyx":240
* return str(v)
*
* cdef class GTFProxy( TupleProxy ): # <<<<<<<<<<<<<<
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict,
const char* function_name, int kw_allowed); /*proto*/
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
+static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/
+static int __Pyx_EndUnpack(PyObject *, Py_ssize_t expected); /*proto*/
+
static void __Pyx_RaiseDoubleKeywordsError(
const char* func_name, PyObject* kw_name); /*proto*/
((likely(PyFloat_CheckExact(obj))) ? \
PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
-
-static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/
-static int __Pyx_EndUnpack(PyObject *, Py_ssize_t expected); /*proto*/
-
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
/* Module declarations from cpython.float */
+/* Module declarations from __builtin__ */
+
/* Module declarations from cpython.complex */
+static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
/* Module declarations from cpython.string */
/* Module declarations from cpython.unicode */
static char *__pyx_f_10TabProxies_StrOrEmpty(char *); /*proto*/
static int __pyx_f_10TabProxies_isNew(char *, char *, size_t); /*proto*/
#define __Pyx_MODULE_NAME "TabProxies"
-int __pyx_module_is_main_TabProxies = 0;
+static int __pyx_module_is_main_TabProxies = 0;
/* Implementation of TabProxies */
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_IndexError;
+static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_xrange;
static PyObject *__pyx_builtin_TypeError;
static char __pyx_k_1[] = "malformatted entry at %s";
static char __pyx_k_2[] = "";
static char __pyx_k_3[] = "out of memory";
-static char __pyx_k_4[] = "incomplete line at %s";
-static char __pyx_k_5[] = "row too large - more than %i fields";
-static char __pyx_k_6[] = "list index out of range";
-static char __pyx_k_7[] = "\t";
-static char __pyx_k_8[] = ".";
-static char __pyx_k_9[] = "\"%s\"";
-static char __pyx_k_10[] = ";";
-static char __pyx_k_11[] = " ";
-static char __pyx_k_12[] = "\"";
-static char __pyx_k_13[] = "%s \"%s\"";
-static char __pyx_k_14[] = "%s %s";
-static char __pyx_k_15[] = "; ";
-static char __pyx_k_16[] = "'GTFProxy' has no attribute '%s'";
-static char __pyx_k_17[] = "field %s not set";
-static char __pyx_k_18[] = "bed format requires at least three columns";
-static char __pyx_k_19[] = "contig of feature.";
-static char __pyx_k_20[] = "feature name.";
-static char __pyx_k_21[] = "feature source.";
-static char __pyx_k_22[] = "feature start (in 0-based open/closed coordinates).";
-static char __pyx_k_23[] = "feature end (in 0-based open/closed coordinates).";
-static char __pyx_k_24[] = "feature score.";
-static char __pyx_k_25[] = "feature strand.";
-static char __pyx_k_26[] = "feature frame.";
-static char __pyx_k_27[] = "feature attributes (as a string).";
-static char __pyx_k_28[] = "TupleProxy._setindex (line 154)";
-static char __pyx_k_29[] = "TupleProxy.__setitem__ (line 177)";
-static char __pyx_k_30[] = "TupleProxy.__next__ (line 192)";
-static char __pyx_k_31[] = "TupleProxy.__str__ (line 202)";
-static char __pyx_k_32[] = "toDot (line 219)";
-static char __pyx_k_33[] = "quote (line 224)";
-static char __pyx_k_34[] = "GTFProxy.asDict (line 350)";
-static char __pyx_k_35[] = "GTFProxy.fromDict (line 385)";
-static char __pyx_k_36[] = "GTFProxy.invert (line 430)";
-static char __pyx_k_37[] = "GTFProxy.keys (line 441)";
-static char __pyx_k_38[] = "GTFProxy.__getattr__ (line 449)";
-static char __pyx_k_39[] = "GTFProxy.setAttribute (line 482)";
-static char __pyx_k_40[] = "NamedTupleProxy.__setattr__ (line 492)";
-static char __pyx_k_41[] = "BedProxy.__setattr__ (line 564)";
-static char __pyx_k_42[] = "VCFProxy.__setattr__ (line 608)";
+static char __pyx_k_5[] = "incomplete line at %s";
+static char __pyx_k_7[] = "row too large - more than %i fields";
+static char __pyx_k_8[] = "list index out of range";
+static char __pyx_k_10[] = "list index out of range %i >= %i";
+static char __pyx_k_14[] = "\t";
+static char __pyx_k_16[] = ".";
+static char __pyx_k_17[] = "\"%s\"";
+static char __pyx_k_18[] = ";";
+static char __pyx_k_20[] = " ";
+static char __pyx_k_22[] = "\"";
+static char __pyx_k_23[] = "%s \"%s\"";
+static char __pyx_k_24[] = "%s %s";
+static char __pyx_k_25[] = "; ";
+static char __pyx_k_29[] = "'GTFProxy' has no attribute '%s'";
+static char __pyx_k_30[] = "field %s not set";
+static char __pyx_k_31[] = "bed format requires at least three columns";
+static char __pyx_k_33[] = "contig of feature.";
+static char __pyx_k_34[] = "feature name.";
+static char __pyx_k_35[] = "feature source.";
+static char __pyx_k_36[] = "feature start (in 0-based open/closed coordinates).";
+static char __pyx_k_37[] = "feature end (in 0-based open/closed coordinates).";
+static char __pyx_k_38[] = "feature score.";
+static char __pyx_k_39[] = "feature strand.";
+static char __pyx_k_40[] = "feature frame.";
+static char __pyx_k_41[] = "feature attributes (as a string).";
static char __pyx_k__id[] = "id";
static char __pyx_k__alt[] = "alt";
static char __pyx_k__end[] = "end";
static char __pyx_k__data[] = "data";
static char __pyx_k__info[] = "info";
static char __pyx_k__join[] = "join";
-static char __pyx_k__keys[] = "keys";
static char __pyx_k__name[] = "name";
static char __pyx_k__qual[] = "qual";
static char __pyx_k__frame[] = "frame";
static char __pyx_k__toDot[] = "toDot";
static char __pyx_k__types[] = "types";
static char __pyx_k__value[] = "value";
+static char __pyx_k__append[] = "append";
static char __pyx_k__asDict[] = "asDict";
static char __pyx_k__contig[] = "contig";
static char __pyx_k__fields[] = "fields";
static char __pyx_k__filter[] = "filter";
static char __pyx_k__format[] = "format";
-static char __pyx_k__invert[] = "invert";
static char __pyx_k__nbytes[] = "nbytes";
static char __pyx_k__offset[] = "offset";
static char __pyx_k__source[] = "source";
static char __pyx_k__xrange[] = "xrange";
static char __pyx_k____str__[] = "__str__";
static char __pyx_k__feature[] = "feature";
+static char __pyx_k__indices[] = "indices";
static char __pyx_k__itemRGB[] = "itemRGB";
static char __pyx_k__nfields[] = "nfields";
-static char __pyx_k__BedProxy[] = "BedProxy";
-static char __pyx_k__GTFProxy[] = "GTFProxy";
static char __pyx_k__KeyError[] = "KeyError";
-static char __pyx_k__VCFProxy[] = "VCFProxy";
static char __pyx_k____main__[] = "__main__";
-static char __pyx_k____next__[] = "__next__";
static char __pyx_k____test__[] = "__test__";
static char __pyx_k__fromDict[] = "fromDict";
static char __pyx_k__thickEnd[] = "thickEnd";
static char __pyx_k__TypeError[] = "TypeError";
+static char __pyx_k___getindex[] = "_getindex";
static char __pyx_k___setindex[] = "_setindex";
static char __pyx_k__bedfields[] = "bedfields";
static char __pyx_k__IndexError[] = "IndexError";
static char __pyx_k__StringType[] = "StringType";
-static char __pyx_k__TupleProxy[] = "TupleProxy";
+static char __pyx_k__TabProxies[] = "TabProxies";
static char __pyx_k__ValueError[] = "ValueError";
static char __pyx_k__attributes[] = "attributes";
static char __pyx_k__blockCount[] = "blockCount";
static char __pyx_k__thickStart[] = "thickStart";
static char __pyx_k__StringTypes[] = "StringTypes";
static char __pyx_k____getattr__[] = "__getattr__";
-static char __pyx_k____setattr__[] = "__setattr__";
static char __pyx_k____setitem__[] = "__setitem__";
static char __pyx_k__blockStarts[] = "blockStarts";
static char __pyx_k__is_modified[] = "is_modified";
static char __pyx_k__getMaxFields[] = "getMaxFields";
-static char __pyx_k__setAttribute[] = "setAttribute";
static char __pyx_k__StopIteration[] = "StopIteration";
static char __pyx_k__map_key2field[] = "map_key2field";
static char __pyx_k__AttributeError[] = "AttributeError";
-static char __pyx_k__NamedTupleProxy[] = "NamedTupleProxy";
static char __pyx_k__hasOwnAttributes[] = "hasOwnAttributes";
static PyObject *__pyx_kp_s_1;
static PyObject *__pyx_kp_s_10;
-static PyObject *__pyx_kp_s_11;
-static PyObject *__pyx_kp_s_12;
-static PyObject *__pyx_kp_s_13;
static PyObject *__pyx_kp_s_14;
-static PyObject *__pyx_kp_s_15;
static PyObject *__pyx_kp_s_16;
static PyObject *__pyx_kp_s_17;
static PyObject *__pyx_kp_s_18;
static PyObject *__pyx_kp_s_2;
-static PyObject *__pyx_kp_u_28;
-static PyObject *__pyx_kp_u_29;
+static PyObject *__pyx_kp_s_20;
+static PyObject *__pyx_kp_s_22;
+static PyObject *__pyx_kp_s_23;
+static PyObject *__pyx_kp_s_24;
+static PyObject *__pyx_kp_s_25;
+static PyObject *__pyx_kp_s_29;
static PyObject *__pyx_kp_s_3;
-static PyObject *__pyx_kp_u_30;
-static PyObject *__pyx_kp_u_31;
-static PyObject *__pyx_kp_u_32;
-static PyObject *__pyx_kp_u_33;
-static PyObject *__pyx_kp_u_34;
-static PyObject *__pyx_kp_u_35;
-static PyObject *__pyx_kp_u_36;
-static PyObject *__pyx_kp_u_37;
-static PyObject *__pyx_kp_u_38;
-static PyObject *__pyx_kp_u_39;
-static PyObject *__pyx_kp_s_4;
-static PyObject *__pyx_kp_u_40;
-static PyObject *__pyx_kp_u_41;
-static PyObject *__pyx_kp_u_42;
+static PyObject *__pyx_kp_s_30;
+static PyObject *__pyx_kp_s_31;
static PyObject *__pyx_kp_s_5;
-static PyObject *__pyx_kp_s_6;
static PyObject *__pyx_kp_s_7;
static PyObject *__pyx_kp_s_8;
-static PyObject *__pyx_kp_s_9;
static PyObject *__pyx_n_s__AttributeError;
-static PyObject *__pyx_n_s__BedProxy;
-static PyObject *__pyx_n_s__GTFProxy;
static PyObject *__pyx_n_s__IndexError;
static PyObject *__pyx_n_s__KeyError;
-static PyObject *__pyx_n_s__NamedTupleProxy;
static PyObject *__pyx_n_s__StopIteration;
static PyObject *__pyx_n_s__StringType;
static PyObject *__pyx_n_s__StringTypes;
-static PyObject *__pyx_n_s__TupleProxy;
+static PyObject *__pyx_n_s__TabProxies;
static PyObject *__pyx_n_s__TypeError;
-static PyObject *__pyx_n_s__VCFProxy;
static PyObject *__pyx_n_s__ValueError;
static PyObject *__pyx_n_s____getattr__;
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PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_10TabProxies_10TupleProxy___dealloc__(o);
+ __pyx_pf_10TabProxies_10TupleProxy_1__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
static int __pyx_mp_ass_subscript_10TabProxies_TupleProxy(PyObject *o, PyObject *i, PyObject *v) {
if (v) {
- return __pyx_pf_10TabProxies_10TupleProxy___setitem__(o, i, v);
+ return __pyx_pf_10TabProxies_10TupleProxy_5__setitem__(o, i, v);
}
else {
PyErr_Format(PyExc_NotImplementedError,
}
static PyMethodDef __pyx_methods_10TabProxies_TupleProxy[] = {
- {__Pyx_NAMESTR("_setindex"), (PyCFunction)__pyx_pf_10TabProxies_10TupleProxy__setindex, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_10TupleProxy__setindex)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_10TabProxies_10TupleProxy___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_10TabProxies_10TupleProxy___next__)},
+ {__Pyx_NAMESTR("_getindex"), (PyCFunction)__pyx_pf_10TabProxies_10TupleProxy_2_getindex, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_10TupleProxy_2_getindex)},
+ {__Pyx_NAMESTR("_setindex"), (PyCFunction)__pyx_pf_10TabProxies_10TupleProxy_4_setindex, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_10TupleProxy_4_setindex)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_10TabProxies_10TupleProxy_8__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_10TabProxies_10TupleProxy_8__next__)},
{0, 0, 0, 0}
};
};
static PySequenceMethods __pyx_tp_as_sequence_TupleProxy = {
- __pyx_pf_10TabProxies_10TupleProxy___len__, /*sq_length*/
+ __pyx_pf_10TabProxies_10TupleProxy_6__len__, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
__pyx_sq_item_10TabProxies_TupleProxy, /*sq_item*/
};
static PyMappingMethods __pyx_tp_as_mapping_TupleProxy = {
- __pyx_pf_10TabProxies_10TupleProxy___len__, /*mp_length*/
- __pyx_pf_10TabProxies_10TupleProxy___getitem__, /*mp_subscript*/
+ __pyx_pf_10TabProxies_10TupleProxy_6__len__, /*mp_length*/
+ __pyx_pf_10TabProxies_10TupleProxy_3__getitem__, /*mp_subscript*/
__pyx_mp_ass_subscript_10TabProxies_TupleProxy, /*mp_ass_subscript*/
};
#endif
};
-PyTypeObject __pyx_type_10TabProxies_TupleProxy = {
+static PyTypeObject __pyx_type_10TabProxies_TupleProxy = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("TabProxies.TupleProxy"), /*tp_name*/
sizeof(struct __pyx_obj_10TabProxies_TupleProxy), /*tp_basicsize*/
&__pyx_tp_as_mapping_TupleProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pf_10TabProxies_10TupleProxy___str__, /*tp_str*/
+ __pyx_pf_10TabProxies_10TupleProxy_9__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_TupleProxy, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
__Pyx_DOCSTR("Proxy class for access to parsed row as a tuple.\n\n This class represents a table row for fast read-access.\n\n Access to individual fields is via the [] operator.\n \n Only read-only access is implemented.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_10TabProxies_10TupleProxy___iter__, /*tp_iter*/
- __pyx_pf_10TabProxies_10TupleProxy___next__, /*tp_iternext*/
+ __pyx_pf_10TabProxies_10TupleProxy_7__iter__, /*tp_iter*/
+ __pyx_pf_10TabProxies_10TupleProxy_8__next__, /*tp_iternext*/
__pyx_methods_10TabProxies_TupleProxy, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_10TabProxies_8GTFProxy___dealloc__(o);
+ __pyx_pf_10TabProxies_8GTFProxy_1__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
PyObject *v = PyObject_GenericGetAttr(o, n);
if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) {
PyErr_Clear();
- v = __pyx_pf_10TabProxies_8GTFProxy___getattr__(o, n);
+ v = __pyx_pf_10TabProxies_8GTFProxy_8__getattr__(o, n);
}
return v;
}
static int __pyx_setprop_10TabProxies_8GTFProxy_contig(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_6contig___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_6contig_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_feature(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_7feature___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_7feature_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_source(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_6source___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_6source_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_start(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_5start___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_5start_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_end(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_3end___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_3end_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_score(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_5score___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_5score_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_strand(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_6strand___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_6strand_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_frame(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_5frame___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_5frame_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_attributes(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_10attributes___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_10attributes_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyMethodDef __pyx_methods_10TabProxies_GTFProxy[] = {
- {__Pyx_NAMESTR("asDict"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_asDict, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_asDict)},
- {__Pyx_NAMESTR("fromDict"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_fromDict, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_fromDict)},
- {__Pyx_NAMESTR("invert"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_invert, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_invert)},
- {__Pyx_NAMESTR("keys"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_keys, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_keys)},
- {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy___getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy___getattr__)},
- {__Pyx_NAMESTR("setAttribute"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_setAttribute, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_setAttribute)},
+ {__Pyx_NAMESTR("asDict"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_2asDict, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_2asDict)},
+ {__Pyx_NAMESTR("fromDict"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_3fromDict, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_3fromDict)},
+ {__Pyx_NAMESTR("invert"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_5invert, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_5invert)},
+ {__Pyx_NAMESTR("keys"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_6keys, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_6keys)},
+ {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_8__getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_8__getattr__)},
+ {__Pyx_NAMESTR("setAttribute"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_9setAttribute, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_9setAttribute)},
{0, 0, 0, 0}
};
static struct PyGetSetDef __pyx_getsets_10TabProxies_GTFProxy[] = {
- {(char *)"contig", __pyx_getprop_10TabProxies_8GTFProxy_contig, __pyx_setprop_10TabProxies_8GTFProxy_contig, __Pyx_DOCSTR(__pyx_k_19), 0},
- {(char *)"feature", __pyx_getprop_10TabProxies_8GTFProxy_feature, __pyx_setprop_10TabProxies_8GTFProxy_feature, __Pyx_DOCSTR(__pyx_k_20), 0},
- {(char *)"source", __pyx_getprop_10TabProxies_8GTFProxy_source, __pyx_setprop_10TabProxies_8GTFProxy_source, __Pyx_DOCSTR(__pyx_k_21), 0},
- {(char *)"start", __pyx_getprop_10TabProxies_8GTFProxy_start, __pyx_setprop_10TabProxies_8GTFProxy_start, __Pyx_DOCSTR(__pyx_k_22), 0},
- {(char *)"end", __pyx_getprop_10TabProxies_8GTFProxy_end, __pyx_setprop_10TabProxies_8GTFProxy_end, __Pyx_DOCSTR(__pyx_k_23), 0},
- {(char *)"score", __pyx_getprop_10TabProxies_8GTFProxy_score, __pyx_setprop_10TabProxies_8GTFProxy_score, __Pyx_DOCSTR(__pyx_k_24), 0},
- {(char *)"strand", __pyx_getprop_10TabProxies_8GTFProxy_strand, __pyx_setprop_10TabProxies_8GTFProxy_strand, __Pyx_DOCSTR(__pyx_k_25), 0},
- {(char *)"frame", __pyx_getprop_10TabProxies_8GTFProxy_frame, __pyx_setprop_10TabProxies_8GTFProxy_frame, __Pyx_DOCSTR(__pyx_k_26), 0},
- {(char *)"attributes", __pyx_getprop_10TabProxies_8GTFProxy_attributes, __pyx_setprop_10TabProxies_8GTFProxy_attributes, __Pyx_DOCSTR(__pyx_k_27), 0},
+ {(char *)"contig", __pyx_getprop_10TabProxies_8GTFProxy_contig, __pyx_setprop_10TabProxies_8GTFProxy_contig, __Pyx_DOCSTR(__pyx_k_33), 0},
+ {(char *)"feature", __pyx_getprop_10TabProxies_8GTFProxy_feature, __pyx_setprop_10TabProxies_8GTFProxy_feature, __Pyx_DOCSTR(__pyx_k_34), 0},
+ {(char *)"source", __pyx_getprop_10TabProxies_8GTFProxy_source, __pyx_setprop_10TabProxies_8GTFProxy_source, __Pyx_DOCSTR(__pyx_k_35), 0},
+ {(char *)"start", __pyx_getprop_10TabProxies_8GTFProxy_start, __pyx_setprop_10TabProxies_8GTFProxy_start, __Pyx_DOCSTR(__pyx_k_36), 0},
+ {(char *)"end", __pyx_getprop_10TabProxies_8GTFProxy_end, __pyx_setprop_10TabProxies_8GTFProxy_end, __Pyx_DOCSTR(__pyx_k_37), 0},
+ {(char *)"score", __pyx_getprop_10TabProxies_8GTFProxy_score, __pyx_setprop_10TabProxies_8GTFProxy_score, __Pyx_DOCSTR(__pyx_k_38), 0},
+ {(char *)"strand", __pyx_getprop_10TabProxies_8GTFProxy_strand, __pyx_setprop_10TabProxies_8GTFProxy_strand, __Pyx_DOCSTR(__pyx_k_39), 0},
+ {(char *)"frame", __pyx_getprop_10TabProxies_8GTFProxy_frame, __pyx_setprop_10TabProxies_8GTFProxy_frame, __Pyx_DOCSTR(__pyx_k_40), 0},
+ {(char *)"attributes", __pyx_getprop_10TabProxies_8GTFProxy_attributes, __pyx_setprop_10TabProxies_8GTFProxy_attributes, __Pyx_DOCSTR(__pyx_k_41), 0},
{0, 0, 0, 0, 0}
};
static PyMappingMethods __pyx_tp_as_mapping_GTFProxy = {
0, /*mp_length*/
- __pyx_pf_10TabProxies_8GTFProxy___getitem__, /*mp_subscript*/
+ __pyx_pf_10TabProxies_8GTFProxy_7__getitem__, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
#endif
};
-PyTypeObject __pyx_type_10TabProxies_GTFProxy = {
+static PyTypeObject __pyx_type_10TabProxies_GTFProxy = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("TabProxies.GTFProxy"), /*tp_name*/
sizeof(struct __pyx_obj_10TabProxies_GTFProxy), /*tp_basicsize*/
&__pyx_tp_as_mapping_GTFProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pf_10TabProxies_8GTFProxy___str__, /*tp_str*/
+ __pyx_pf_10TabProxies_8GTFProxy_4__str__, /*tp_str*/
__pyx_tp_getattro_10TabProxies_GTFProxy, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_GTFProxy, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
__Pyx_DOCSTR("Proxy class for access to GTF fields.\n\n This class represents a GTF entry for fast read-access.\n Write-access has been added as well, though some care must\n be taken. If any of the string fields (contig, source, ...)\n are set, the new value is tied to the lifetime of the\n argument that was supplied.\n\n The only exception is the attributes field when set from\n a dictionary - this field will manage its own memory.\n\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
PyObject *v = PyObject_GenericGetAttr(o, n);
if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) {
PyErr_Clear();
- v = __pyx_pf_10TabProxies_15NamedTupleProxy___getattr__(o, n);
+ v = __pyx_pf_10TabProxies_15NamedTupleProxy_1__getattr__(o, n);
}
return v;
}
}
static PyMethodDef __pyx_methods_10TabProxies_NamedTupleProxy[] = {
- {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pf_10TabProxies_15NamedTupleProxy___getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pf_10TabProxies_15NamedTupleProxy_1__getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(0)},
{0, 0, 0, 0}
};
#endif
};
-PyTypeObject __pyx_type_10TabProxies_NamedTupleProxy = {
+static PyTypeObject __pyx_type_10TabProxies_NamedTupleProxy = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("TabProxies.NamedTupleProxy"), /*tp_name*/
sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), /*tp_basicsize*/
__pyx_tp_getattro_10TabProxies_NamedTupleProxy, /*tp_getattro*/
__pyx_tp_setattro_10TabProxies_NamedTupleProxy, /*tp_setattro*/
&__pyx_tp_as_buffer_NamedTupleProxy, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
0, /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
static int __pyx_tp_setattro_10TabProxies_BedProxy(PyObject *o, PyObject *n, PyObject *v) {
if (v) {
- return __pyx_pf_10TabProxies_8BedProxy___setattr__(o, n, v);
+ return __pyx_pf_10TabProxies_8BedProxy_1__setattr__(o, n, v);
}
else {
if (__pyx_ptype_10TabProxies_NamedTupleProxy->tp_setattro)
#endif
};
-PyTypeObject __pyx_type_10TabProxies_BedProxy = {
+static PyTypeObject __pyx_type_10TabProxies_BedProxy = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("TabProxies.BedProxy"), /*tp_name*/
sizeof(struct __pyx_obj_10TabProxies_BedProxy), /*tp_basicsize*/
0, /*tp_getattro*/
__pyx_tp_setattro_10TabProxies_BedProxy, /*tp_setattro*/
&__pyx_tp_as_buffer_BedProxy, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
__Pyx_DOCSTR("Proxy class for access to Bed fields.\n\n This class represents a GTF entry for fast read-access.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
static int __pyx_tp_setattro_10TabProxies_VCFProxy(PyObject *o, PyObject *n, PyObject *v) {
if (v) {
- return __pyx_pf_10TabProxies_8VCFProxy___setattr__(o, n, v);
+ return __pyx_pf_10TabProxies_8VCFProxy_2__setattr__(o, n, v);
}
else {
if (__pyx_ptype_10TabProxies_NamedTupleProxy->tp_setattro)
}
}
+static PyObject *__pyx_getprop_10TabProxies_8VCFProxy_pos(PyObject *o, void *x) {
+ return __pyx_pf_10TabProxies_8VCFProxy_3pos___get__(o);
+}
+
static PyMethodDef __pyx_methods_10TabProxies_VCFProxy[] = {
{0, 0, 0, 0}
};
+static struct PyGetSetDef __pyx_getsets_10TabProxies_VCFProxy[] = {
+ {(char *)"pos", __pyx_getprop_10TabProxies_8VCFProxy_pos, 0, __Pyx_DOCSTR(__pyx_k_37), 0},
+ {0, 0, 0, 0, 0}
+};
+
static PyNumberMethods __pyx_tp_as_number_VCFProxy = {
0, /*nb_add*/
0, /*nb_subtract*/
};
static PySequenceMethods __pyx_tp_as_sequence_VCFProxy = {
- __pyx_pf_10TabProxies_8VCFProxy___len__, /*sq_length*/
+ __pyx_pf_10TabProxies_8VCFProxy_1__len__, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_item*/
};
static PyMappingMethods __pyx_tp_as_mapping_VCFProxy = {
- __pyx_pf_10TabProxies_8VCFProxy___len__, /*mp_length*/
+ __pyx_pf_10TabProxies_8VCFProxy_1__len__, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
#endif
};
-PyTypeObject __pyx_type_10TabProxies_VCFProxy = {
+static PyTypeObject __pyx_type_10TabProxies_VCFProxy = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("TabProxies.VCFProxy"), /*tp_name*/
sizeof(struct __pyx_obj_10TabProxies_VCFProxy), /*tp_basicsize*/
0, /*tp_getattro*/
__pyx_tp_setattro_10TabProxies_VCFProxy, /*tp_setattro*/
&__pyx_tp_as_buffer_VCFProxy, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
__Pyx_DOCSTR("Proxy class for access to VCF fields.\n\n The genotypes are accessed via index.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_iternext*/
__pyx_methods_10TabProxies_VCFProxy, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_10TabProxies_VCFProxy, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
};
static PyMethodDef __pyx_methods[] = {
- {__Pyx_NAMESTR("toDot"), (PyCFunction)__pyx_pf_10TabProxies_toDot, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_toDot)},
- {__Pyx_NAMESTR("quote"), (PyCFunction)__pyx_pf_10TabProxies_quote, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_quote)},
{0, 0, 0, 0}
};
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+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_3));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_15));
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+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_18));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_19));
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+ *
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+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_20));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_21));
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+ /* "TabProxies.pyx":416
+ * self.attributes = <char *>calloc( l + 1, sizeof(char) )
+ * if self.attributes == NULL:
+ * raise ValueError("out of memory" ) # <<<<<<<<<<<<<<
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+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_26));
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+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_3));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_26));
+
+ /* "TabProxies.pyx":454
+ * '''return a list of attributes defined in this entry.'''
+ * r = self.attributes
+ * return [ x.strip().split(" ")[0] for x in r.split(";") if x.strip() != '' ] # <<<<<<<<<<<<<<
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+ * def __getitem__(self, key):
+ */
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+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_18));
+ PyTuple_SET_ITEM(__pyx_k_tuple_27, 0, ((PyObject *)__pyx_kp_s_18));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_18));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_27));
+ __pyx_k_tuple_28 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_28));
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_20));
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+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_20));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_28));
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+ PyTuple_SET_ITEM(__pyx_k_tuple_32, 0, ((PyObject *)__pyx_kp_s_31));
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+ __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_2 = PyInt_FromLong(2); if (unlikely(!__pyx_int_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+ __pyx_int_4 = PyInt_FromLong(4); if (unlikely(!__pyx_int_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+ return 0;
+ __pyx_L1_error:;
+ return -1;
+}
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+PyMODINIT_FUNC initTabProxies(void); /*proto*/
PyMODINIT_FUNC initTabProxies(void)
#else
PyMODINIT_FUNC PyInit_TabProxies(void); /*proto*/
{
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
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void* __pyx_refnanny = NULL;
__Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
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if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Constants init code ---*/
+ if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Global init code ---*/
/*--- Function export code ---*/
/*--- Type init code ---*/
__pyx_vtabptr_10TabProxies_TupleProxy = &__pyx_vtable_10TabProxies_TupleProxy;
- #if PY_MAJOR_VERSION >= 3
__pyx_vtable_10TabProxies_TupleProxy.getMaxFields = (int (*)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t))__pyx_f_10TabProxies_10TupleProxy_getMaxFields;
__pyx_vtable_10TabProxies_TupleProxy.take = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_take;
__pyx_vtable_10TabProxies_TupleProxy.present = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_present;
__pyx_vtable_10TabProxies_TupleProxy.copy = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_copy;
__pyx_vtable_10TabProxies_TupleProxy.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_update;
- #else
- *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.getMaxFields = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_getMaxFields;
- *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.take = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_take;
- *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.present = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_present;
- *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.copy = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_copy;
- *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.update = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_update;
- #endif
if (PyType_Ready(&__pyx_type_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_TupleProxy, "__setitem__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_10TupleProxy___setitem__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_10TupleProxy___setitem__.doc = __pyx_doc_10TabProxies_10TupleProxy___setitem__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy___setitem__;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy_5__setitem__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy_5__setitem__.doc = __pyx_doc_10TabProxies_10TupleProxy_5__setitem__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy_5__setitem__;
}
}
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_TupleProxy, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_10TupleProxy___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_10TupleProxy___next__.doc = __pyx_doc_10TabProxies_10TupleProxy___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy___next__;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy_8__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy_8__next__.doc = __pyx_doc_10TabProxies_10TupleProxy_8__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy_8__next__;
}
}
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_TupleProxy, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_10TupleProxy___str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_10TupleProxy___str__.doc = __pyx_doc_10TabProxies_10TupleProxy___str__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy___str__;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy_9__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy_9__str__.doc = __pyx_doc_10TabProxies_10TupleProxy_9__str__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy_9__str__;
}
}
if (__Pyx_SetVtable(__pyx_type_10TabProxies_TupleProxy.tp_dict, __pyx_vtabptr_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_10TabProxies_TupleProxy = &__pyx_type_10TabProxies_TupleProxy;
__pyx_vtabptr_10TabProxies_GTFProxy = &__pyx_vtable_10TabProxies_GTFProxy;
__pyx_vtable_10TabProxies_GTFProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_TupleProxy;
- #if PY_MAJOR_VERSION >= 3
__pyx_vtable_10TabProxies_GTFProxy.__pyx_base.getMaxFields = (int (*)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t))__pyx_f_10TabProxies_8GTFProxy_getMaxFields;
__pyx_vtable_10TabProxies_GTFProxy.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_8GTFProxy_update;
- #else
- *(void(**)(void))&__pyx_vtable_10TabProxies_GTFProxy.__pyx_base.getMaxFields = (void(*)(void))__pyx_f_10TabProxies_8GTFProxy_getMaxFields;
- *(void(**)(void))&__pyx_vtable_10TabProxies_GTFProxy.__pyx_base.update = (void(*)(void))__pyx_f_10TabProxies_8GTFProxy_update;
- #endif
__pyx_type_10TabProxies_GTFProxy.tp_base = __pyx_ptype_10TabProxies_TupleProxy;
- if (PyType_Ready(&__pyx_type_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_GTFProxy, "__getattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_GTFProxy, "__getattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_8GTFProxy___getattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_8GTFProxy___getattr__.doc = __pyx_doc_10TabProxies_8GTFProxy___getattr__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8GTFProxy___getattr__;
+ __pyx_wrapperbase_10TabProxies_8GTFProxy_8__getattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_8GTFProxy_8__getattr__.doc = __pyx_doc_10TabProxies_8GTFProxy_8__getattr__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8GTFProxy_8__getattr__;
}
}
- if (__Pyx_SetVtable(__pyx_type_10TabProxies_GTFProxy.tp_dict, __pyx_vtabptr_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "GTFProxy", (PyObject *)&__pyx_type_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_10TabProxies_GTFProxy.tp_dict, __pyx_vtabptr_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "GTFProxy", (PyObject *)&__pyx_type_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_10TabProxies_GTFProxy = &__pyx_type_10TabProxies_GTFProxy;
__pyx_vtabptr_10TabProxies_NamedTupleProxy = &__pyx_vtable_10TabProxies_NamedTupleProxy;
__pyx_vtable_10TabProxies_NamedTupleProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_TupleProxy;
__pyx_type_10TabProxies_NamedTupleProxy.tp_base = __pyx_ptype_10TabProxies_TupleProxy;
- if (PyType_Ready(&__pyx_type_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_NamedTupleProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_NamedTupleProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_10TabProxies_15NamedTupleProxy___setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_10TabProxies_15NamedTupleProxy___setattr__.doc = __pyx_doc_10TabProxies_15NamedTupleProxy___setattr__;
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_15NamedTupleProxy___setattr__;
}
}
- if (__Pyx_SetVtable(__pyx_type_10TabProxies_NamedTupleProxy.tp_dict, __pyx_vtabptr_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "NamedTupleProxy", (PyObject *)&__pyx_type_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_10TabProxies_NamedTupleProxy.tp_dict, __pyx_vtabptr_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "NamedTupleProxy", (PyObject *)&__pyx_type_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_10TabProxies_NamedTupleProxy = &__pyx_type_10TabProxies_NamedTupleProxy;
__pyx_vtabptr_10TabProxies_BedProxy = &__pyx_vtable_10TabProxies_BedProxy;
__pyx_vtable_10TabProxies_BedProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
- #if PY_MAJOR_VERSION >= 3
__pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.getMaxFields = (int (*)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t))__pyx_f_10TabProxies_8BedProxy_getMaxFields;
__pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_8BedProxy_update;
- #else
- *(void(**)(void))&__pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.getMaxFields = (void(*)(void))__pyx_f_10TabProxies_8BedProxy_getMaxFields;
- *(void(**)(void))&__pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.update = (void(*)(void))__pyx_f_10TabProxies_8BedProxy_update;
- #endif
__pyx_type_10TabProxies_BedProxy.tp_base = __pyx_ptype_10TabProxies_NamedTupleProxy;
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+ if (PyType_Ready(&__pyx_type_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
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+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_BedProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
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- __pyx_wrapperbase_10TabProxies_8BedProxy___setattr__.doc = __pyx_doc_10TabProxies_8BedProxy___setattr__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8BedProxy___setattr__;
+ __pyx_wrapperbase_10TabProxies_8BedProxy_1__setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_8BedProxy_1__setattr__.doc = __pyx_doc_10TabProxies_8BedProxy_1__setattr__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8BedProxy_1__setattr__;
}
}
- if (__Pyx_SetVtable(__pyx_type_10TabProxies_BedProxy.tp_dict, __pyx_vtabptr_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "BedProxy", (PyObject *)&__pyx_type_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_10TabProxies_BedProxy.tp_dict, __pyx_vtabptr_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "BedProxy", (PyObject *)&__pyx_type_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_10TabProxies_BedProxy = &__pyx_type_10TabProxies_BedProxy;
__pyx_vtabptr_10TabProxies_VCFProxy = &__pyx_vtable_10TabProxies_VCFProxy;
__pyx_vtable_10TabProxies_VCFProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
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__pyx_vtable_10TabProxies_VCFProxy.__pyx_base.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_8VCFProxy_update;
- #else
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- #endif
__pyx_type_10TabProxies_VCFProxy.tp_base = __pyx_ptype_10TabProxies_NamedTupleProxy;
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+ if (PyType_Ready(&__pyx_type_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
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+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_VCFProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
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- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8VCFProxy___setattr__;
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+ __pyx_wrapperbase_10TabProxies_8VCFProxy_2__setattr__.doc = __pyx_doc_10TabProxies_8VCFProxy_2__setattr__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8VCFProxy_2__setattr__;
}
}
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+ if (__Pyx_SetVtable(__pyx_type_10TabProxies_VCFProxy.tp_dict, __pyx_vtabptr_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "VCFProxy", (PyObject *)&__pyx_type_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_10TabProxies_VCFProxy = &__pyx_type_10TabProxies_VCFProxy;
/*--- Type import code ---*/
__pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Function import code ---*/
/*--- Execution code ---*/
- /* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":1
+ /* "TabProxies.pyx":1
* import types # <<<<<<<<<<<<<<
* from cpython cimport PyString_FromStringAndSize, PyString_AsString, PyString_AS_STRING
*
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__types, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":490
+ /* "TabProxies.pyx":228
+ * return result
+ *
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+ * '''convert value to '.' if None'''
+ * if v == None: return "."
+ */
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+ __Pyx_GOTREF(__pyx_t_1);
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+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ /* "TabProxies.pyx":233
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+ /* "TabProxies.pyx":495
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PyType_Modified(__pyx_ptype_10TabProxies_NamedTupleProxy);
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__Pyx_GOTREF(((PyObject *)__pyx_t_1));
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__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
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+ /* "cpython/type.pxd":2
*
* cdef extern from "Python.h": # <<<<<<<<<<<<<<
* # The C structure of the objects used to describe built-in types.
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
if (__pyx_m) {
__Pyx_AddTraceback("init TabProxies");
Py_DECREF(__pyx_m); __pyx_m = 0;
return result;
}
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+
+ tmp_type = tstate->curexc_type;
+ tmp_value = tstate->curexc_value;
+ tmp_tb = tstate->curexc_traceback;
+ tstate->curexc_type = type;
+ tstate->curexc_value = value;
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->curexc_type;
+ *value = tstate->curexc_value;
+ *tb = tstate->curexc_traceback;
+
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+}
+
+
+#if PY_MAJOR_VERSION < 3
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ Py_XINCREF(type);
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ /* First, check the traceback argument, replacing None with NULL. */
+ if (tb == Py_None) {
+ Py_DECREF(tb);
+ tb = 0;
+ }
+ else if (tb != NULL && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ /* Next, replace a missing value with None */
+ if (value == NULL) {
+ value = Py_None;
+ Py_INCREF(value);
+ }
+ #if PY_VERSION_HEX < 0x02050000
+ if (!PyClass_Check(type))
+ #else
+ if (!PyType_Check(type))
+ #endif
+ {
+ /* Raising an instance. The value should be a dummy. */
+ if (value != Py_None) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ /* Normalize to raise <class>, <instance> */
+ Py_DECREF(value);
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+ if (PyInstance_Check(type)) {
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+ Py_INCREF(type);
+ }
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
+ #else
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+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ #endif
+ }
+
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+
+#else /* Python 3+ */
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ if (tb == Py_None) {
+ tb = 0;
+ } else if (tb && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto bad;
+ }
+ if (value == Py_None)
+ value = 0;
+
+ if (PyExceptionInstance_Check(type)) {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto bad;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(value);
+ } else if (!PyExceptionClass_Check(type)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto bad;
+ }
+
+ PyErr_SetObject(type, value);
+
+ if (tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* tmp_tb = tstate->curexc_traceback;
+ if (tb != tmp_tb) {
+ Py_INCREF(tb);
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_tb);
+ }
+ }
+
+bad:
+ return;
+}
+#endif
+
static void __Pyx_RaiseArgtupleInvalid(
const char* func_name,
int exact,
return 0;
}
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+ PyErr_Format(PyExc_ValueError,
+ #if PY_VERSION_HEX < 0x02050000
+ "need more than %d value%s to unpack", (int)index,
+ #else
+ "need more than %zd value%s to unpack", index,
+ #endif
+ (index == 1) ? "" : "s");
+}
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ #if PY_VERSION_HEX < 0x02050000
+ "too many values to unpack (expected %d)", (int)expected);
+ #else
+ "too many values to unpack (expected %zd)", expected);
+ #endif
+}
+
+static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) {
+ PyObject *item;
+ if (!(item = PyIter_Next(iter))) {
+ if (!PyErr_Occurred()) {
+ __Pyx_RaiseNeedMoreValuesError(index);
+ }
+ }
+ return item;
+}
+
+static int __Pyx_EndUnpack(PyObject *iter, Py_ssize_t expected) {
+ PyObject *item;
+ if ((item = PyIter_Next(iter))) {
+ Py_DECREF(item);
+ __Pyx_RaiseTooManyValuesError(expected);
+ return -1;
+ }
+ else if (!PyErr_Occurred())
+ return 0;
+ else
+ return -1;
+}
+
static void __Pyx_RaiseDoubleKeywordsError(
const char* func_name,
PyObject* kw_name)
return (double)-1;
}
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
- PyErr_Format(PyExc_ValueError,
- #if PY_VERSION_HEX < 0x02050000
- "need more than %d value%s to unpack", (int)index,
- #else
- "need more than %zd value%s to unpack", index,
- #endif
- (index == 1) ? "" : "s");
-}
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- #if PY_VERSION_HEX < 0x02050000
- "too many values to unpack (expected %d)", (int)expected);
- #else
- "too many values to unpack (expected %zd)", expected);
- #endif
-}
-
-static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) {
- PyObject *item;
- if (!(item = PyIter_Next(iter))) {
- if (!PyErr_Occurred()) {
- __Pyx_RaiseNeedMoreValuesError(index);
- }
- }
- return item;
-}
-
-static int __Pyx_EndUnpack(PyObject *iter, Py_ssize_t expected) {
- PyObject *item;
- if ((item = PyIter_Next(iter))) {
- Py_DECREF(item);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- }
- else if (!PyErr_Occurred())
- return 0;
- else
- return -1;
-}
-
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
return module;
}
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
-
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-}
-
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
-
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-}
-
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- /* First, check the traceback argument, replacing None with NULL. */
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- /* Next, replace a missing value with None */
- if (value == NULL) {
- value = Py_None;
- Py_INCREF(value);
- }
- #if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
- #else
- if (!PyType_Check(type))
- #endif
- {
- /* Raising an instance. The value should be a dummy. */
- if (value != Py_None) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- /* Normalize to raise <class>, <instance> */
- Py_DECREF(value);
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
-
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-
-#else /* Python 3+ */
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
-
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
-
- PyErr_SetObject(type, value);
-
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-
-bad:
- return;
-}
-#endif
-
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
const int is_unsigned = const_zero < neg_one;
if (!result)
goto bad;
if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
+ PyErr_Format(PyExc_TypeError,
"%s.%s is not a type object",
module_name, class_name);
goto bad;
}
if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
+ PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
#if PY_VERSION_HEX < 0x02050000
#endif
}
else if (((PyTypeObject *)result)->tp_basicsize != size) {
- PyErr_Format(PyExc_ValueError,
+ PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
goto bad;
cdef bint is_modified
cdef int getMaxFields( self, size_t nbytes )
+# cdef char * _getindex( self, int idx )
cdef take( self, char * buffer, size_t nbytes )
cdef present( self, char * buffer, size_t nbytes )
self.nfields = field
- def __getitem__( self, key ):
-
- cdef int i = key
+ def _getindex( self, int index ):
+ '''return item at idx index'''
+ cdef int i = index
if i < 0: i += self.nfields
if i < 0: raise IndexError( "list index out of range" )
i += self.offset
if i >= self.nfields:
- raise IndexError( "list index out of range" )
+ raise IndexError( "list index out of range %i >= %i" % (i, self.nfields ))
return self.fields[i]
+ def __getitem__( self, key ):
+ if type(key) == int: return self._getindex( key )
+ # slice object
+ start, end, step = key.indices( self.nfields )
+ result = []
+ for index in range( start, end, step ):
+ result.append( self._getindex( index ) )
+ return result
+
def _setindex( self, index, value ):
'''set item at idx index.'''
cdef int idx = index
self.start = atoi( cstart ) - 1
self.end = atoi( cend )
-
+ self.nfields = 9
+
property contig:
'''contig of feature.'''
def __get__( self ): return self.contig
r = self.attributes
return [ x.strip().split(" ")[0] for x in r.split(";") if x.strip() != '' ]
- def __getitem__(self, item):
- return self.__getattr__( item )
+ def __getitem__(self, key):
+ return self.__getattr__( key )
def __getattr__(self, item ):
"""Generic lookup of attribute from GFF/GTF attributes
start += strlen(query) + 1
# skip gaps before
- while start[0] == " ": start += 1
+ while start[0] == ' ': start += 1
if start[0] == '"':
start += 1
end = start
while end[0] != '\0' and end[0] != '"': end += 1
- l = end - start + 1
- cpy = <char*>calloc( l, sizeof(char ) )
- if cpy == NULL: raise ValueError("out of memory" )
- memcpy( cpy, start, l )
- cpy[l-1] = '\0'
- result = cpy
- free(cpy)
+ l = end - start
+ result = PyString_FromStringAndSize( start, l )
return result
else:
return start
self.contig = self.fields[0]
# vcf counts from 1 - correct here
self.pos = atoi( self.fields[1] ) - 1
-
+
def __len__(self):
return max(0, self.nfields - 9)
+ property pos:
+ '''feature end (in 0-based open/closed coordinates).'''
+ def __get__( self ):
+ return self.pos
+
def __setattr__(self, key, value ):
'''set attribute.'''
if key == "pos":
cdef int idx
idx, f = self.map_key2field[key]
TupleProxy._setindex(self, idx, str(value) )
-
+
+++ /dev/null
-#
-# Code to read, write and edit VCF files
-#
-# VCF lines are encoded as a dictionary with these keys (note: all lowercase):
-# 'chrom': string
-# 'pos': integer
-# 'id': string
-# 'ref': string
-# 'alt': list of strings
-# 'qual': integer
-# 'filter': None (missing value), or list of keys (strings); empty list parsed as ["PASS"]
-# 'info': dictionary of values (see below)
-# 'format': list of keys (strings)
-# sample keys: dictionary of values (see below)
-#
-# The sample keys are accessible through vcf.getsamples()
-#
-# A dictionary of values contains value keys (defined in ##INFO or ##FORMAT lines) which map
-# to a list, containign integers, floats, strings, or characters. Missing values are replaced
-# by a particular value, often -1 or .
-#
-# Genotypes are not stored as a string, but as a list of 1 or 3 elements (for haploid and diploid samples),
-# the first (and last) the integer representing an allele, and the second the separation character.
-# Note that there is just one genotype per sample, but for consistency the single element is stored in a list.
-#
-# Header lines other than ##INFO, ##FORMAT and ##FILTER are stored as (key, value) pairs and are accessible
-# through getheader()
-#
-# The VCF class can be instantiated with a 'regions' variable consisting of tuples (chrom,start,end) encoding
-# 0-based half-open segments. Only variants with a position inside the segment will be parsed. A regions
-# parser is available under parse_regions.
-#
-# When instantiated, a reference can be passed to the VCF class. This may be any class that supports a
-# fetch(chrom, start, end) method.
-#
-#
-#
-# NOTE: the position that is returned to Python is 0-based, NOT 1-based as in the VCF file.
-#
-#
-#
-# TODO:
-# only v4.0 writing is complete; alleles are not converted to v3.3 format
-#
-
-from collections import namedtuple, defaultdict
-from operator import itemgetter
-import sys, re, copy, bisect
-
-import pysam
-
-gtsRegEx = re.compile("[|/\\\\]")
-alleleRegEx = re.compile('^[ACGTN]+$')
-
-# Utility function. Uses 0-based coordinates
-def get_sequence(chrom, start, end, fa):
- # obtain sequence from .fa file, without truncation
- if end<=start: return ""
- if not fa: return "N"*(end-start)
- if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
- sequence = fa.fetch(chrom, start, end).upper()
- if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
- return sequence
-
-# Utility function. Parses a region string
-def parse_regions( string ):
- result = []
- for r in string.split(','):
- elts = r.split(':')
- chrom, start, end = elts[0], 0, 3000000000
- if len(elts)==1: pass
- elif len(elts)==2:
- if len(elts[1])>0:
- ielts = elts[1].split('-')
- if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
- try: start, end = int(ielts[0])-1, int(ielts[1])
- except: raise ValueError("Don't understand region string '%s'" % r)
- else:
- raise ValueError("Don't understand region string '%s'" % r)
- result.append( (chrom,start,end) )
- return result
-
-
-FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue')
-
-###########################################################################################################
-#
-# New class
-#
-###########################################################################################################
-
-class VCFRecord:
- '''vcf record.
-
- initialized from data and vcf meta
- '''
-
- data = None
- vcf = None
-
- def __init__(self, data, vcf):
- self.data, self.vcf = data, vcf
-
- if len(data) != len(self.vcf._samples):
- self.error(str(data),
- self.BAD_NUMBER_OF_COLUMNS,
- "expected %s for %s samples (%s), got %s" % \
- (len(self.vcf._samples),
- len(self.vcf._samples),
- self.vcf._samples,
- len(data)))
-
- property contig:
- def contig( self ): return self.data[0]
-
- property pos:
- def __get__( self ):
- return self.data.pos
-
- property id:
- def __get__( self ): return self.data[2]
-
- property ref:
- def __get__(self ):
- # note: gerton substitutes reference if it can be fixed.
- return self.data[3].upper()
-
- property alt:
- def __get__(self):
- # convert v3.3 to v4.0 alleles below
- alt = self.data[4]
- if alt == ".": alt = []
- else: alt = alt.upper().split(',')
- return alt
-
- property qual:
- def __get__(self):
- qual = self.data[5]
- if qual == ".": qual = -1
- else:
- try: qual = float(qual)
- except: self.error(line,self.QUAL_NOT_NUMERICAL)
-
- property filter:
- def __get__(self):
- # postpone checking that filters exist. Encode missing filter or no filtering as empty list
- if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = []
- else: filter = cols[6].split(';')
-
- return filter
-
- property info:
- def __get__(self):
- col = self.data[7]
- # dictionary of keys, and list of values
- info = {}
- if col != ".":
- for blurp in col.split(';'):
- elts = blurp.split('=')
- if len(elts) == 1: v = None
- elif len(elts) == 2: v = elts[1]
- else: self.error(str(self.data),self.ERROR_INFO_STRING)
- info[elts[0]] = self.parse_formatdata(elts[0], v, self.vcf._info, line)
- return info
-
- property format:
- def __get__(self):
- return self.data[8].split(':')
-
- def __getitem__(self, key):
-
- # parse sample columns
- values = self.data[self.vcf._sample2column[key]].split(':')
- alt = self.alt
- format = self.format
-
- if len(values) > len(format):
- self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
-
- result = {}
- for idx in range(len(format)):
- expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
- if idx < len(values): value = values[idx]
- else:
- if expected == -1: value = "."
- else: value = ",".join(["."]*expected)
-
- result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, line)
- if expected != -1 and len(result[format[idx]]) != expected:
- self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
- "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
- if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]]))
- result[format[idx]] = result[format[idx]][:expected]
-
- return result
-
- def __str__(self):
- return str(self.data)
-
-class VCF:
-
- # types
- NT_UNKNOWN = 0
- NT_NUMBER = 1
- NT_ALLELES = 2
- NT_NR_ALLELES = 3
- NT_GENOTYPES = 4
- NT_PHASED_GENOTYPES = 5
-
- _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier",
- 1:"BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string",
- 2:"BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s",
- 3:"BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)",
- 4:"POS_NOT_NUMERICAL:Position column is not numerical",
- 5:"UNKNOWN_CHAR_IN_REF:Unknown character in reference field",
- 6:"V33_BAD_REF:Reference should be single-character in v3.3 VCF",
- 7:"V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF",
- 8:"POS_NOT_POSITIVE:Position field must be >0",
- 9:"QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'",
- 10:"ERROR_INFO_STRING:Error while parsing info field",
- 11:"ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)",
- 12:"ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s",
- 13:"ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string",
- 14:"FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header",
- 15:"FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header",
- 16:"BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)",
- 17:"BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)",
- 18:"BAD_GENOTYPE:Cannot parse genotype (%s)",
- 19:"V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)",
- 20:"MISSING_REF:Reference allele missing",
- 21:"V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)",
- 22:"V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets",
- 23:"FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes",
- 24:"V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields",
- 25:"HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs",
- 26:"WRONG_REF:Wrong reference %s",
- 27:"ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data",
- 28:"BAD_CHR_TAG:Error calculating chr tag for %s",
- 29:"ZERO_LENGTH_ALLELE:Found zero-length allele",
- 30:"MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base"
- }
-
- # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields
- _header = []
-
- # version number; 33=v3.3; 40=v4.0
- _version = 40
-
- # info, filter and format data
- _info = {}
- _filter = {}
- _format = {}
-
- # header; and required columns
- _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]
- _samples = []
-
- # control behaviour
- _ignored_errors = set([11]) # ERROR_UNKNOWN_KEY
- _warn_errors = set([])
- _leftalign = False
-
- # reference sequence
- _reference = None
-
- # regions to include; None includes everything
- _regions = None
-
- # statefull stuff
- _lineno = -1
- _line = None
- _lines = None
-
- def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False):
- # make error identifiers accessible by name
- for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id
- if _copy != None:
- self._leftalign = _copy._leftalign
- self._header = _copy._header[:]
- self._version = _copy._version
- self._info = copy.deepcopy(_copy._info)
- self._filter = copy.deepcopy(_copy._filter)
- self._format = copy.deepcopy(_copy._format)
- self._samples = _copy._samples[:]
- self._sample2column = copy.deepcopy(_copy._sample2column)
- self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
- self._warn_errors = copy.deepcopy(_copy._warn_errors)
- self._reference = _copy._reference
- self._regions = _copy._regions
- if reference: self._reference = reference
- if regions: self._regions = regions
- if leftalign: self._leftalign = leftalign
- self._lines = lines
-
- def error(self,line,error,opt=None):
- if error in self._ignored_errors: return
- errorlabel, errorstring = self._errors[error].split(':')
- if opt: errorstring = errorstring % opt
- errwarn = ["Error","Warning"][error in self._warn_errors]
- sys.stderr.write("Line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring))
- if error in self._warn_errors: return
- raise ValueError(errorstring)
-
- def parse_format(self,line,format,filter=False):
- if self._version == 40:
- if not format.startswith('<'):
- self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
- format = "<"+format
- if not format.endswith('>'):
- self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
- format += ">"
- format = format[1:-1]
- data = {'id':None,'number':None,'type':None,'descr':None}
- idx = 0
- while len(format.strip())>0:
- elts = format.strip().split(',')
- first, rest = elts[0], ','.join(elts[1:])
- if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
- if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
- if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- first = ["ID=","Number=","Type=","Description="][idx] + first
- if first.startswith('ID='): data['id'] = first.split('=')[1]
- elif first.startswith('Number='): data['number'] = first.split('=')[1]
- elif first.startswith('Type='): data['type'] = first.split('=')[1]
- elif first.startswith('Description='):
- elts = format.split('"')
- if len(elts)<3:
- self.error(line,self.FORMAT_MISSING_QUOTES)
- elts = first.split('=') + [rest]
- data['descr'] = elts[1]
- rest = '"'.join(elts[2:])
- if rest.startswith(','): rest = rest[1:]
- else:
- self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- format = rest
- idx += 1
- if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings
- if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- if not data['descr']:
- self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- data['descr'] = '<none>'
- if not data['type'] and not data['number']:
- # fine, ##filter format
- return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
- if not data['type'] in ["Integer","Float","Character","String","Flag"]:
- self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- # I would like a missing-value field, but it isn't there
- if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value
- else: data['missing'] = '.'
- if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- try:
- n = int(data['number'])
- t = self.NT_NUMBER
- except ValueError:
- n = -1
- if data['number'] == '.': t = self.NT_UNKNOWN
- elif data['number'] == '#alleles': t = self.NT_ALLELES
- elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES
- elif data['number'] == '#genotypes': t = self.NT_GENOTYPES
- elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
- else:
- self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
-
-
- def format_format( self, fmt, filter=False ):
- values = [('ID',fmt.id)]
- if fmt.number != None and not filter:
- if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
- elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
- elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
- elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
- elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes"
- elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes"
- else:
- raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
- values.append( ('Number',nmb) )
- values.append( ('Type', fmt.type) )
- values.append( ('Description', '"' + fmt.description + '"') )
- if self._version == 33:
- format = ",".join(v for k,v in values)
- else:
- format = "<" + (",".join( "%s=%s" % (k,v) for (k,v) in values )) + ">"
- return format
-
- def get_expected(self, format, formatdict, alt):
- fmt = formatdict[format]
- if fmt.numbertype == self.NT_UNKNOWN: return -1
- if fmt.numbertype == self.NT_NUMBER: return fmt.number
- if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
- if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
- if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
- if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1)
- return 0
-
-
- def _add_definition(self, formatdict, key, data, line ):
- if key in formatdict: return
- self.error(line,self.ERROR_UNKNOWN_KEY,key)
- if data == None:
- formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
- return
- if data == []: data = [""] # unsure what type -- say string
- if type(data[0]) == type(0.0):
- formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
- return
- if type(data[0]) == type(0):
- formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
- return
- formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".")
-
-
- # todo: trim trailing missing values
- def format_formatdata( self, data, format, key=True, value=True, separator=":" ):
- output, sdata = [], []
- if type(data) == type([]): # for FORMAT field, make data with dummy values
- d = {}
- for k in data: d[k] = []
- data = d
- # convert missing values; and silently add definitions if required
- for k in data:
- self._add_definition( format, k, data[k], "(output)" )
- for idx,v in enumerate(data[k]):
- if v == format[k].missingvalue: data[k][idx] = "."
- # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
- for k in data:
- if k != 'GT': sdata.append( (k,data[k]) )
- sdata.sort()
- if 'GT' in data:
- sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
- for k,v in sdata:
- if v == []: v = None
- if key and value:
- if v != None: output.append( k+"="+','.join(map(str,v)) )
- else: output.append( k )
- elif key: output.append(k)
- elif value:
- if v != None: output.append( ','.join(map(str,v)) )
- else: output.append( "." ) # should not happen
- # snip off trailing missing data
- while len(output) > 1:
- last = output[-1].replace(',','').replace('.','')
- if len(last)>0: break
- output = output[:-1]
- return separator.join(output)
-
-
- def enter_default_format(self):
- for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
- FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
- FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
- FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
- FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.')]:
- if f.id not in self._format:
- self._format[f.id] = f
-
- def parse_header( self, line ):
- assert line.startswith('##')
- elts = line[2:].split('=')
- key = elts[0].strip()
- value = '='.join(elts[1:]).strip()
- if key == "fileformat":
- if value == "VCFv3.3":
- self._version = 33
- elif value == "VCFv4.0":
- self._version = 40
- elif value == "VCFv4.1":
- # AH - for testing
- self._version = 40
- else:
- self.error(line,self.UNKNOWN_FORMAT_STRING)
- elif key == "INFO":
- f = self.parse_format(line, value)
- self._info[ f.id ] = f
- elif key == "FILTER":
- f = self.parse_format(line, value, filter=True)
- self._filter[ f.id ] = f
- elif key == "FORMAT":
- f = self.parse_format(line, value)
- self._format[ f.id ] = f
- else:
- # keep other keys in the header field
- self._header.append( (key,value) )
-
-
- def write_header( self, stream ):
- stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
- for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
- for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]:
- for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER"))))
-
-
- def parse_heading( self, line ):
- assert line.startswith('#')
- assert not line.startswith('##')
- headings = line[1:].split('\t')
- if len(headings)==1 and len(line[1:].split()) >= 9:
- self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS)
- headings = line[1:].split()
-
- for i,s in enumerate(self._required):
-
- if len(headings)<=i or headings[i] != s:
-
- if len(headings) <= i:
- err = "(%sth entry not found)" % (i+1)
- else:
- err = "(found %s, expected %s)" % (headings[i],s)
-
- #self.error(line,self.BADLY_FORMATTED_HEADING,err)
-
- # allow FORMAT column to be absent
- if len(headings) == 8:
- headings.append("FORMAT")
- else:
- self.error(line,self.BADLY_FORMATTED_HEADING,err)
-
- self._samples = headings[9:]
- self._sample2column = dict( [(y,x) for x,y in enumerate( self._samples ) ] )
-
- def write_heading( self, stream ):
- stream.write("#" + "\t".join(self._required + self._samples) + "\n")
-
- def convertGT(self, GTstring):
- if GTstring == ".": return ["."]
- try:
- gts = gtsRegEx.split(GTstring)
- if len(gts) == 1: return [int(gts[0])]
- if len(gts) != 2: raise ValueError()
- if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
- return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
- except ValueError:
- self.error(self._line,self.BAD_GENOTYPE,GTstring)
- return [".","|","."]
-
-
- def convertGTback(self, GTdata):
- return ''.join(map(str,GTdata))
-
- def parse_formatdata( self, key, value, formatdict, line ):
- # To do: check that the right number of values is present
- f = formatdict.get(key,None)
- if f == None:
- self._add_definition(formatdict, key, value, line )
- f = formatdict[key]
- if f.type == "Flag":
- if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
- return []
- values = value.split(',')
- # deal with trailing data in some early VCF files
- if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
- self.error(line,self.ERROR_TRAILING_DATA,values[-1])
- values[-1] = values[-1].split(';')[0]
- if f.type == "Integer":
- for idx,v in enumerate(values):
- try:
- if v == ".": values[idx] = f.missingvalue
- else: values[idx] = int(v)
- except:
- self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,values)
- return [0] * len(values)
- return values
- elif f.type == "String":
- self._line = line
- if f.id == "GT": values = map( self.convertGT, values )
- return values
- elif f.type == "Character":
- for v in values:
- if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
- return values
- elif f.type == "Float":
- for idx,v in enumerate(values):
- if v == ".": values[idx] = f.missingvalue
- try: return map(float,values)
- except:
- self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,values)
- return [0.0] * len(values)
- else:
- # can't happen
- self.error(line,self.ERROR_INFO_STRING)
-
-
- def inregion(self, chrom, pos):
- if not self._regions: return True
- for r in self._regions:
- if r[0] == chrom and r[1] <= pos < r[2]: return True
- return False
-
-
- def parse_data( self, line, lineparse=False ):
- cols = line.split('\t')
- if len(cols) != len(self._samples)+9:
- # gracefully deal with absent FORMAT column
- if len(cols) == 8 and len(self._samples)==0:
- cols.append("")
- else:
- self.error(line,
- self.BAD_NUMBER_OF_COLUMNS,
- "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols)))
-
- chrom = cols[0]
-
- # get 0-based position
- try: pos = int(cols[1])-1
- except: self.error(line,self.POS_NOT_NUMERICAL)
- if pos < 0: self.error(line,self.POS_NOT_POSITIVE)
-
- # implement filtering
- if not self.inregion(chrom,pos): return None
-
- # end of first-pass parse for sortedVCF
- if lineparse: return chrom, pos, line
-
- id = cols[2]
-
- ref = cols[3].upper()
- if ref == ".":
- self.error(line,self.MISSING_REF)
- if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
- else: ref = ""
- else:
- for c in ref:
- if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF)
- if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference)
-
- # make sure reference is sane
- if self._reference:
- left = max(0,pos-100)
- faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
- faref = faref_leftflank[pos-left:]
- if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
- ref = faref
-
- # convert v3.3 to v4.0 alleles below
- if cols[4] == ".": alt = []
- else: alt = cols[4].upper().split(',')
-
- if cols[5] == ".": qual = -1
- else:
- try: qual = float(cols[5])
- except: self.error(line,self.QUAL_NOT_NUMERICAL)
-
- # postpone checking that filters exist. Encode missing filter or no filtering as empty list
- if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = []
- else: filter = cols[6].split(';')
-
- # dictionary of keys, and list of values
- info = {}
- if cols[7] != ".":
- for blurp in cols[7].split(';'):
- elts = blurp.split('=')
- if len(elts) == 1: v = None
- elif len(elts) == 2: v = elts[1]
- else: self.error(line,self.ERROR_INFO_STRING)
- info[elts[0]] = self.parse_formatdata(elts[0], v, self._info, line)
-
- # Gracefully deal with absent FORMAT column
- if cols[8] == "": format = []
- else: format = cols[8].split(':')
-
- # check: all filters are defined
- for f in filter:
- if f not in self._filter: self.error(line,self.FILTER_NOT_DEFINED, f)
-
- # check: format fields are defined
- for f in format:
- if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f)
-
- # convert v3.3 alleles
- if self._version == 33:
- if len(ref) != 1: self.error(line,self.V33_BAD_REF)
- newalts = []
- have_deletions = False
- for a in alt:
- if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
- elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
- elif a.startswith('D'): # allow D<seq> and D<num>
- have_deletions = True
- try:
- l = int(a[1:]) # throws ValueError if sequence
- if len(ref) < l: # add to reference if necessary
- addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
- ref += addns
- for i,na in enumerate(newalts): newalts[i] = na+addns
- a = ref[l:] # new deletion, deleting pos...pos+l
- except ValueError:
- s = a[1:]
- if len(ref) < len(s): # add Ns to reference if necessary
- addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
- if not s.endswith(addns) and addns != 'N'*len(addns):
- self.error(line,self.V33_UNMATCHED_DELETION,
- "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
- ref += addns
- for i,na in enumerate(newalts): newalts[i] = na+addns
- a = ref[len(s):] # new deletion, deleting from pos
- else:
- self.error(line,self.V33_BAD_ALLELE)
- newalts.append(a)
- alt = newalts
- # deletion alleles exist, add dummy 1st reference allele, and account for leading base
- if have_deletions:
- if pos == 0:
- # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
- addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
- ref += addn
- alt = [allele+addn for allele in alt]
- else:
- addn = get_sequence(chrom,pos-1,pos,self._reference)
- ref = addn + ref
- alt = [addn + allele for allele in alt]
- pos -= 1
- else:
- # format v4.0 -- just check for nucleotides
- for allele in alt:
- if not alleleRegEx.match(allele):
- self.error(line,self.V40_BAD_ALLELE,allele)
-
- # check for leading nucleotide in indel calls
- for allele in alt:
- if len(allele) != len(ref):
- if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
- if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
- self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
-
- # trim trailing bases in alleles
- for i in range(1,min(len(ref),min(map(len,alt)))):
- if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
- break
- ref, alt = ref[:-1], [allele[:-1] for allele in alt]
-
- # left-align alleles, if a reference is available
- if self._leftalign and self._reference:
- while left < pos:
- movable = True
- for allele in alt:
- if len(allele) > len(ref):
- longest, shortest = allele, ref
- else:
- longest, shortest = ref, allele
- if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
- movable = False
- if longest[-1].upper() != longest[len(shortest)-1].upper():
- movable = False
- if not movable:
- break
- ref = ref[:-1]
- alt = [allele[:-1] for allele in alt]
- if min(len(allele) for allele in alt) == 0 or len(ref) == 0:
- ref = faref_leftflank[pos-left-1] + ref
- alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
- pos -= 1
-
- # parse sample columns
- samples = []
- for sample in cols[9:]:
- dict = {}
- values = sample.split(':')
- if len(values) > len(format):
- self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
- for idx in range(len(format)):
- expected = self.get_expected(format[idx], self._format, alt)
- if idx < len(values): value = values[idx]
- else:
- if expected == -1: value = "."
- else: value = ",".join(["."]*expected)
- dict[format[idx]] = self.parse_formatdata(format[idx], value, self._format, line)
- if expected != -1 and len(dict[format[idx]]) != expected:
- self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
- "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
- if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
- dict[format[idx]] = dict[format[idx]][:expected]
- samples.append( dict )
-
- # done
- d = {'chrom':chrom,
- 'pos':pos, # return 0-based position
- 'id':id,
- 'ref':ref,
- 'alt':alt,
- 'qual':qual,
- 'filter':filter,
- 'info':info,
- 'format':format}
- for key,value in zip(self._samples,samples):
- d[key] = value
-
- return d
-
-
- def write_data(self, stream, data):
- required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
- for k in required:
- if k not in data: raise ValueError("Required key %s not found in data" % str(k))
- if data['alt'] == []: alt = "."
- else: alt = ",".join(data['alt'])
- if data['filter'] == None: filter = "."
- elif data['filter'] == []:
- if self._version == 33: filter = "0"
- else: filter = "PASS"
- else: filter = ';'.join(data['filter'])
- if data['qual'] == -1: qual = "."
- else: qual = str(data['qual'])
-
- output = [data['chrom'],
- str(data['pos']+1), # change to 1-based position
- data['id'],
- data['ref'],
- alt,
- qual,
- filter,
- self.format_formatdata( data['info'], self._info, separator=";" ),
- self.format_formatdata( data['format'], self._format, value=False ) ]
-
- for s in self._samples:
- output.append( self.format_formatdata( data[s], self._format, key=False ) )
-
- stream.write( "\t".join(output) + "\n" )
-
- def _parse_header(self, stream):
- self._lineno = 0
- for line in stream:
- self._lineno += 1
- if line.startswith('##'):
- self.parse_header( line.strip() )
- elif line.startswith('#'):
- self.parse_heading( line.strip() )
- self.enter_default_format()
- else:
- break
- return line
-
- def _parse(self, line, stream):
- if len(line.strip()) > 0:
- d = self.parse_data( line.strip() )
- if d: yield d
- for line in stream:
- self._lineno += 1
- if self._lines and self._lineno > self._lines: raise StopIteration
- d = self.parse_data( line.strip() )
- if d: yield d
-
- ######################################################################################################
- #
- # API follows
- #
- ######################################################################################################
-
- def getsamples(self):
- """ List of samples in VCF file """
- return self._samples
-
- def setsamples(self,samples):
- """ List of samples in VCF file """
- self._samples = samples
-
- def getheader(self):
- """ List of header key-value pairs (strings) """
- return self._header
-
- def setheader(self,header):
- """ List of header key-value pairs (strings) """
- self._header = header
-
- def getinfo(self):
- """ Dictionary of ##INFO tags, as VCF.FORMAT values """
- return self._info
-
- def setinfo(self,info):
- """ Dictionary of ##INFO tags, as VCF.FORMAT values """
- self._info = info
-
- def getformat(self):
- """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
- return self._format
-
- def setformat(self,format):
- """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
- self._format = format
-
- def getfilter(self):
- """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
- return self._filter
-
- def setfilter(self,filter):
- """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
- self._filter = filter
-
- def setversion(self, version):
- if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files")
- self._version = version
-
- def setregions(self, regions):
- self._regions = regions
-
- def setreference(self, ref):
- """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """
- self._reference = ref
-
- def ignoreerror(self, errorstring):
- try: self._ignored_errors.add(self.__dict__[errorstring])
- except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
-
- def warnerror(self, errorstring):
- try: self._warn_errors.add(self.__dict__[errorstring])
- except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
-
- def parse(self, stream):
- """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
- last_line = self._parse_header(stream)
- # now return a generator that does the actual work. In this way the pre-processing is done
- # before the first piece of data is yielded
- return self._parse(last_line, stream)
-
- def write(self, stream, datagenerator):
- """ Writes a VCF file to a stream, using a data generator (or list) """
- self.write_header(stream)
- self.write_heading(stream)
- for data in datagenerator: self.write_data(stream,data)
-
- def writeheader(self, stream):
- """ Writes a VCF header """
- self.write_header(stream)
- self.write_heading(stream)
-
- def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2):
- """ Utility function: compares two calls for equality """
- # a variant should always be assigned to a unique position, one base before
- # the leftmost position of the alignment gap. If this rule is implemented
- # correctly, the two positions must be equal for the calls to be identical.
- if pos1 != pos2: return False
- # from both calls, trim rightmost bases when identical. Do this safely, i.e.
- # only when the reference bases are not Ns
- while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]:
- ref1 = ref1[:-1]
- alt1 = alt1[:-1]
- while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
- ref2 = ref2[:-1]
- alt2 = alt2[:-1]
- # now, the alternative alleles must be identical
- return alt1 == alt2
-
-###########################################################################################################
-###########################################################################################################
-## API functions added by Andreas
-###########################################################################################################
-
- def connect( self, filename ):
- '''connect to tabix file.'''
- self.tabixfile = pysam.Tabixfile( filename )
- self._parse_header(self.tabixfile.header)
-
- def fetch(self,
- reference = None,
- start = None,
- end = None,
- region = None ):
- """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
-
- iter = self.tabixfile.fetch( reference, start, end, region, parser = pysam.asVCF() )
- for x in iter:
- yield VCFRecord( x, self )
-
- def validate( self, record ):
- '''validate vcf record.
-
- returns a validated record.
- '''
-
- chrom, pos = record.chrom, record.pos
-
- # check reference
- ref = record.ref
- if ref == ".":
- self.error(str(record),self.MISSING_REF)
- if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
- else: ref = ""
- else:
- for c in ref:
- if c not in "ACGTN": self.error(str(record),self.UNKNOWN_CHAR_IN_REF)
- if "N" in ref: ref = get_sequence(chrom,
- pos,
- pos+len(ref),
- self._reference)
-
- # make sure reference is sane
- if self._reference:
- left = max(0,self.pos-100)
- faref_leftflank = get_sequence(chrom,left,self.pos+len(ref),self._reference)
- faref = faref_leftflank[pos-left:]
- if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
- ref = faref
-
- # check: format fields are defined
- for f in record.format:
- if f not in self._format: self.error(str(record),self.FORMAT_NOT_DEFINED, f)
-
- # check: all filters are defined
- for f in record.filter:
- if f not in self._filter: self.error(str(record),self.FILTER_NOT_DEFINED, f)
-
- # convert v3.3 alleles
- if self._version == 33:
- if len(ref) != 1: self.error(line,self.V33_BAD_REF)
- newalts = []
- have_deletions = False
- for a in alt:
- if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
- elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
- elif a.startswith('D'): # allow D<seq> and D<num>
- have_deletions = True
- try:
- l = int(a[1:]) # throws ValueError if sequence
- if len(ref) < l: # add to reference if necessary
- addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
- ref += addns
- for i,na in enumerate(newalts): newalts[i] = na+addns
- a = ref[l:] # new deletion, deleting pos...pos+l
- except ValueError:
- s = a[1:]
- if len(ref) < len(s): # add Ns to reference if necessary
- addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
- if not s.endswith(addns) and addns != 'N'*len(addns):
- self.error(line,self.V33_UNMATCHED_DELETION,
- "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
- ref += addns
- for i,na in enumerate(newalts): newalts[i] = na+addns
- a = ref[len(s):] # new deletion, deleting from pos
- else:
- self.error(line,self.V33_BAD_ALLELE)
- newalts.append(a)
- alt = newalts
- # deletion alleles exist, add dummy 1st reference allele, and account for leading base
- if have_deletions:
- if pos == 0:
- # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
- addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
- ref += addn
- alt = [allele+addn for allele in alt]
- else:
- addn = get_sequence(chrom,pos-1,pos,self._reference)
- ref = addn + ref
- alt = [addn + allele for allele in alt]
- pos -= 1
- else:
- # format v4.0 -- just check for nucleotides
- for allele in alt:
- if not alleleRegEx.match(allele):
- self.error(line,self.V40_BAD_ALLELE,allele)
-
-
- # check for leading nucleotide in indel calls
- for allele in alt:
- if len(allele) != len(ref):
- if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
- if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
- self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
-
- # trim trailing bases in alleles
- for i in range(1,min(len(ref),min(map(len,alt)))):
- if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
- break
- ref, alt = ref[:-1], [allele[:-1] for allele in alt]
-
- # left-align alleles, if a reference is available
- if self._leftalign and self._reference:
- while left < pos:
- movable = True
- for allele in alt:
- if len(allele) > len(ref):
- longest, shortest = allele, ref
- else:
- longest, shortest = ref, allele
- if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
- movable = False
- if longest[-1].upper() != longest[len(shortest)-1].upper():
- movable = False
- if not movable:
- break
- ref = ref[:-1]
- alt = [allele[:-1] for allele in alt]
- if min(len(allele) for allele in alt) == 0 or len(ref) == 0:
- ref = faref_leftflank[pos-left-1] + ref
- alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
- pos -= 1
-
-
-
-
#
# import is a python reserved word.
SAMTOOLS_DISPATCH = {
+ # samtools 'documented' commands
"view" : ( "view", None ),
"sort" : ( "sort", None),
- "samimport": ( "import", None),
- "pileup" : ( "pileup", ( (("-c",), Pileup.iterate ), ), ),
+ "mpileup" : ( "mpileup", None),
+ "depth" : ("depth", None),
"faidx" : ("faidx", None),
"tview" : ("tview", None),
"index" : ("index", None),
+ "idxstats" : ("idxstats", None),
"fixmate" : ("fixmate", None),
- "glfview" : ("glfview", None),
"flagstat" : ("flagstat", None),
"calmd" : ("calmd", None),
"merge" : ("merge", None),
- "rmdup" : ("rmdup", None) }
+ "rmdup" : ("rmdup", None),
+ "reheader" : ("reheader", None),
+ "cat" : ("cat", None),
+ "targetcut" : ("targetcut", None),
+ "phase" : ("phase", None),
+ # others
+ "samimport": ( "import", None),
+ "bam2fq" : ("bam2fq", None),
+ # obsolete
+ # "pileup" : ( "pileup", ( (("-c",), Pileup.iterate ), ), ),
+
+ }
# instantiate samtools commands as python functions
for key, options in SAMTOOLS_DISPATCH.iteritems():
-/* Generated by Cython 0.13 on Tue Jun 7 17:24:36 2011 */
+/* Generated by Cython 0.14.1 on Fri Nov 25 19:51:23 2011 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#define PyBytes_Repr PyString_Repr
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
+#endif
+
+#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#endif
-
#ifndef PySet_CheckExact
-# define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
+ #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
+#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+
#if PY_MAJOR_VERSION >= 3
+ #define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
#define PyInt_Check(op) PyLong_Check(op)
#define PyInt_CheckExact(op) PyLong_CheckExact(op)
#endif
#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
+ #define PyBoolObject PyLongObject
#endif
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
#endif
+#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
+ #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
+ #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
+#else
+ #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
+ #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
+#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
#include "stdint.h"
#include "bam.h"
#include "sam.h"
-#include "glf.h"
-#include "bam_maqcns.h"
#include "faidx.h"
#include "pysam_util.h"
#include "pythread.h"
+#ifdef PYREX_WITHOUT_ASSERTIONS
+#define CYTHON_WITHOUT_ASSERTIONS
+#endif
+
+
/* inline attribute */
#ifndef CYTHON_INLINE
#if defined(__GNUC__)
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
#define CYTHON_INLINE inline
#else
- #define CYTHON_INLINE
+ #define CYTHON_INLINE
#endif
#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
# endif
# elif defined(__ICC) || defined(__INTEL_COMPILER)
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
-# define CYTHON_UNUSED
+# define CYTHON_UNUSED
# endif
#endif
#ifdef __GNUC__
/* Test for GCC > 2.95 */
-#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
+#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
#define likely(x) __builtin_expect(!!(x), 1)
#define unlikely(x) __builtin_expect(!!(x), 0)
#else /* __GNUC__ > 2 ... */
"csamtools.pyx",
"csamtools.pxd",
"bool.pxd",
+ "complex.pxd",
};
/* Type declarations */
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":388
+/* "csamtools.pyx":388
* counter[0] += 1;
*
* ctypedef struct MateData: # <<<<<<<<<<<<<<
uint32_t flag;
} __pyx_t_9csamtools_MateData;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1478
+/* "csamtools.pyx":1537
* ##-------------------------------------------------------------------
* ##-------------------------------------------------------------------
* ctypedef struct __iterdata: # <<<<<<<<<<<<<<
int seq_len;
} __pyx_t_9csamtools___iterdata;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1655
+/* "csamtools.pyx":1717
* bam_plp_set_mask( self.pileup_iter, self.mask )
*
* cdef setupIteratorData( self, # <<<<<<<<<<<<<<
int reopen;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3192
- * bam_maqindel_ret_destroy(self._r)
- *
- * cdef class IndelCallerBase: # <<<<<<<<<<<<<<
- * '''Base class for SNP callers.
- *
- */
-
-struct __pyx_obj_9csamtools_IndelCallerBase {
- PyObject_HEAD
- bam_maqindel_opt_t *options;
- struct __pyx_obj_9csamtools_IteratorColumn *iter;
- int cap_mapQ;
- int max_depth;
-};
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3330
- * return self._call()
- *
- * cdef class IteratorIndelCalls( IndelCallerBase ): # <<<<<<<<<<<<<<
- * """*(IteratorColumn iterator)*
- *
- */
-
-struct __pyx_obj_9csamtools_IteratorIndelCalls {
- struct __pyx_obj_9csamtools_IndelCallerBase __pyx_base;
-};
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":244
- * ## Public methods
- * ######################################################################
- * cdef class Fastafile: # <<<<<<<<<<<<<<
- * '''*(filename)*
- *
- */
-
-struct __pyx_obj_9csamtools_Fastafile {
- PyObject_HEAD
- struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtab;
- char *_filename;
- faidx_t *fastafile;
-};
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3103
- * return call
- *
- * cdef class IndelCall: # <<<<<<<<<<<<<<
- * '''the results of an indel call.'''
- * cdef int _tid
- */
-
-struct __pyx_obj_9csamtools_IndelCall {
- PyObject_HEAD
- int _tid;
- int _pos;
- int _coverage;
- int _rms_mapping_quality;
- bam_maqindel_ret_t *_r;
-};
-
-/* "pysam/csamtools.pxd":388
- * cdef bam1_t * _delegate
- *
- * cdef class Samfile: # <<<<<<<<<<<<<<
- * cdef char * _filename
- * # pointer to samfile
- */
-
-struct __pyx_obj_9csamtools_Samfile {
- PyObject_HEAD
- struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtab;
- char *_filename;
- samfile_t *samfile;
- bam_index_t *index;
- int isbam;
- int isremote;
- bam1_t *b;
- char *mode;
-};
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3287
- * return call
- *
- * cdef class IndelCaller( IndelCallerBase ): # <<<<<<<<<<<<<<
- * '''*(IteratorColumn iterator_column )*
- *
- */
-
-struct __pyx_obj_9csamtools_IndelCaller {
- struct __pyx_obj_9csamtools_IndelCallerBase __pyx_base;
-};
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":91
+/* "csamtools.pyx":91
* return dest
*
* cdef class PileupRead # <<<<<<<<<<<<<<
uint32_t _is_tail;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2816
- * return retval, out_stderr, out_stdout
- *
- * cdef class SNPCall: # <<<<<<<<<<<<<<
- * '''the results of a SNP call.'''
- * cdef int _tid
- */
-
-struct __pyx_obj_9csamtools_SNPCall {
- PyObject_HEAD
- int _tid;
- int _pos;
- char _reference_base;
- char _genotype;
- int _consensus_quality;
- int _snp_quality;
- int _rms_mapping_quality;
- int _coverage;
-};
-
-/* "pysam/csamtools.pxd":383
+/* "csamtools.pxd":423
+ * cdef char * _getrname( self, int tid )
*
- * # need to declare all C fields and methods here
- * cdef class AlignedRead: # <<<<<<<<<<<<<<
+ * cdef class IteratorRow: # <<<<<<<<<<<<<<
+ * pass
*
- * # object that this AlignedRead represents
*/
-struct __pyx_obj_9csamtools_AlignedRead {
+struct __pyx_obj_9csamtools_IteratorRow {
PyObject_HEAD
- bam1_t *_delegate;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1542
- * return ret
- *
- * cdef class IteratorColumn: # <<<<<<<<<<<<<<
- * '''abstract base class for iterators over columns.
+/* "csamtools.pyx":1415
+ * if self.owns_samfile: samclose( self.fp )
*
+ * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
+ * """iterates over all mapped reads by chaining iterators over each reference
+ * """
*/
-struct __pyx_obj_9csamtools_IteratorColumn {
- PyObject_HEAD
- struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtab;
- struct __pyx_obj_9csamtools_IteratorRowRegion *iter;
- int tid;
- int pos;
- int n_plp;
- int mask;
- const bam_pileup1_t * plp;
- bam_plp_t pileup_iter;
- __pyx_t_9csamtools___iterdata iterdata;
+struct __pyx_obj_9csamtools_IteratorRowAllRefs {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
struct __pyx_obj_9csamtools_Samfile *samfile;
- struct __pyx_obj_9csamtools_Fastafile *fastafile;
- PyObject *stepper;
+ int tid;
+ struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1712
- * self.iterdata.seq = NULL
+/* "csamtools.pxd":426
+ * pass
*
- * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
- * '''iterates over a region only.
- * '''
+ * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam1_t * b
+ * cdef samfile_t * fp
*/
-struct __pyx_obj_9csamtools_IteratorColumnRegion {
- struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
+struct __pyx_obj_9csamtools_IteratorRowAll {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtab;
+ bam1_t *b;
+ samfile_t *fp;
+ int owns_samfile;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1187
- * ##-------------------------------------------------------------------
- * ##-------------------------------------------------------------------
- * cdef class IteratorRow: # <<<<<<<<<<<<<<
- * '''abstract base class for iterators over mapped reads.
+/* "csamtools.pyx":82
+ * return dest
*
+ * cdef class PileupProxy # <<<<<<<<<<<<<<
+ * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ):
+ * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
*/
-struct __pyx_obj_9csamtools_IteratorRow {
+struct __pyx_obj_9csamtools_PileupProxy {
PyObject_HEAD
-};
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1356
- * if self.owns_samfile: samclose( self.fp )
- *
- * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
- * """iterates over all mapped reads by chaining iterators over each reference
- * """
- */
-
-struct __pyx_obj_9csamtools_IteratorRowAllRefs {
- struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
- struct __pyx_obj_9csamtools_Samfile *samfile;
+ bam_pileup1_t *plp;
int tid;
- struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter;
+ int pos;
+ int n_pu;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1206
+/* "csamtools.pyx":1265
* pass
*
* cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
int owns_samfile;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1741
- * self.n_plp )
+/* "csamtools.pyx":244
+ * ## Public methods
+ * ######################################################################
+ * cdef class Fastafile: # <<<<<<<<<<<<<<
+ * '''*(filename)*
*
- * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
- * """iterates over all columns by chaining iterators over each reference
- * """
*/
-struct __pyx_obj_9csamtools_IteratorColumnAllRefs {
- struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
+struct __pyx_obj_9csamtools_Fastafile {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtab;
+ char *_filename;
+ faidx_t *fastafile;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1402
+/* "csamtools.pyx":1461
* raise StopIteration
*
* cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
int owns_samfile;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2873
- *
+/* "csamtools.pyx":1601
+ * return ret
*
- * cdef class SNPCallerBase: # <<<<<<<<<<<<<<
- * '''Base class for SNP callers.
+ * cdef class IteratorColumn: # <<<<<<<<<<<<<<
+ * '''abstract base class for iterators over columns.
*
*/
-struct __pyx_obj_9csamtools_SNPCallerBase {
+struct __pyx_obj_9csamtools_IteratorColumn {
PyObject_HEAD
- struct __pyx_vtabstruct_9csamtools_SNPCallerBase *__pyx_vtab;
- bam_maqcns_t *c;
- struct __pyx_obj_9csamtools_IteratorColumn *iter;
+ struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtab;
+ struct __pyx_obj_9csamtools_IteratorRowRegion *iter;
+ int tid;
+ int pos;
+ int n_plp;
+ int mask;
+ const bam_pileup1_t * plp;
+ bam_plp_t pileup_iter;
+ __pyx_t_9csamtools___iterdata iterdata;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
+ struct __pyx_obj_9csamtools_Fastafile *fastafile;
+ PyObject *stepper;
+ int max_depth;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3021
- * return call
- *
- * cdef class SNPCaller( SNPCallerBase ): # <<<<<<<<<<<<<<
- * '''*(IteratorColumn iterator_column )*
+/* "csamtools.pyx":1806
+ * self.n_plp )
*
+ * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
+ * """iterates over all columns by chaining iterators over each reference
+ * """
*/
-struct __pyx_obj_9csamtools_SNPCaller {
- struct __pyx_obj_9csamtools_SNPCallerBase __pyx_base;
+struct __pyx_obj_9csamtools_IteratorColumnAllRefs {
+ struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2946
- * sys.stdout.flush()
- *
- * cdef class IteratorSNPCalls( SNPCallerBase ): # <<<<<<<<<<<<<<
- * """*(IteratorColumn iterator)*
+/* "csamtools.pxd":394
+ * cdef bam1_t * _delegate
*
+ * cdef class Samfile: # <<<<<<<<<<<<<<
+ * cdef char * _filename
+ * # pointer to samfile
*/
-struct __pyx_obj_9csamtools_IteratorSNPCalls {
- struct __pyx_obj_9csamtools_SNPCallerBase __pyx_base;
+struct __pyx_obj_9csamtools_Samfile {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtab;
+ char *_filename;
+ samfile_t *samfile;
+ bam_index_t *index;
+ int isbam;
+ int isstream;
+ int isremote;
+ bam1_t *b;
+ char *mode;
+ int64_t start_offset;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1292
- * if self.owns_samfile: samclose( self.fp )
- *
- * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int reopen = True)*
+/* "csamtools.pyx":2902
+ * return retval, out_stderr, out_stdout
*
+ * cdef class SNPCall: # <<<<<<<<<<<<<<
+ * '''the results of a SNP call.'''
+ * cdef int _tid
*/
-struct __pyx_obj_9csamtools_IteratorRowAll {
- struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtab;
- bam1_t *b;
- samfile_t *fp;
- int owns_samfile;
+struct __pyx_obj_9csamtools_SNPCall {
+ PyObject_HEAD
+ int _tid;
+ int _pos;
+ char _reference_base;
+ char _genotype;
+ int _consensus_quality;
+ int _snp_quality;
+ int _rms_mapping_quality;
+ int _coverage;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3370
+/* "csamtools.pyx":3456
*
*
* cdef class IndexedReads: # <<<<<<<<<<<<<<
int owns_samfile;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":82
- * return dest
+/* "csamtools.pyx":1777
+ * self.iterdata.seq = NULL
*
- * cdef class PileupProxy # <<<<<<<<<<<<<<
- * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ):
- * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
+ * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
+ * '''iterates over a region only.
+ * '''
*/
-struct __pyx_obj_9csamtools_PileupProxy {
- PyObject_HEAD
- bam_pileup1_t *plp;
- int tid;
- int pos;
- int n_pu;
+struct __pyx_obj_9csamtools_IteratorColumnRegion {
+ struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
+};
+
+/* "csamtools.pxd":389
+ *
+ * # need to declare all C fields and methods here
+ * cdef class AlignedRead: # <<<<<<<<<<<<<<
+ *
+ * # object that this AlignedRead represents
+ */
+
+struct __pyx_obj_9csamtools_AlignedRead {
+ PyObject_HEAD
+ bam1_t *_delegate;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1542
+/* "csamtools.pyx":1601
* return ret
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtabptr_9csamtools_IteratorColumn;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1712
+/* "csamtools.pyx":1777
* self.iterdata.seq = NULL
*
* cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *__pyx_vtabptr_9csamtools_IteratorColumnRegion;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2873
- *
- *
- * cdef class SNPCallerBase: # <<<<<<<<<<<<<<
- * '''Base class for SNP callers.
- *
- */
-
-struct __pyx_vtabstruct_9csamtools_SNPCallerBase {
- PyObject *(*__dump)(struct __pyx_obj_9csamtools_SNPCallerBase *, glf1_t *, uint32_t, int);
-};
-static struct __pyx_vtabstruct_9csamtools_SNPCallerBase *__pyx_vtabptr_9csamtools_SNPCallerBase;
-
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3021
- * return call
- *
- * cdef class SNPCaller( SNPCallerBase ): # <<<<<<<<<<<<<<
- * '''*(IteratorColumn iterator_column )*
- *
- */
-
-struct __pyx_vtabstruct_9csamtools_SNPCaller {
- struct __pyx_vtabstruct_9csamtools_SNPCallerBase __pyx_base;
-};
-static struct __pyx_vtabstruct_9csamtools_SNPCaller *__pyx_vtabptr_9csamtools_SNPCaller;
-
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1206
+/* "csamtools.pyx":1265
* pass
*
* cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtabptr_9csamtools_IteratorRowRegion;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1402
+/* "csamtools.pyx":1461
* raise StopIteration
*
* cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtabptr_9csamtools_IteratorRowSelection;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1741
+/* "csamtools.pyx":1806
* self.n_plp )
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":415
+/* "csamtools.pyx":415
*
*
* cdef class Samfile: # <<<<<<<<<<<<<<
- * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*
- *
+ * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,
+ * add_sq_text = False )*
*/
struct __pyx_vtabstruct_9csamtools_Samfile {
static struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtabptr_9csamtools_Samfile;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":244
+/* "csamtools.pyx":244
* ## Public methods
* ######################################################################
* cdef class Fastafile: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtabptr_9csamtools_Fastafile;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1292
+/* "csamtools.pyx":1351
* if self.owns_samfile: samclose( self.fp )
*
* cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
};
static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtools_IteratorRowAll;
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2946
- * sys.stdout.flush()
- *
- * cdef class IteratorSNPCalls( SNPCallerBase ): # <<<<<<<<<<<<<<
- * """*(IteratorColumn iterator)*
- *
- */
-
-struct __pyx_vtabstruct_9csamtools_IteratorSNPCalls {
- struct __pyx_vtabstruct_9csamtools_SNPCallerBase __pyx_base;
-};
-static struct __pyx_vtabstruct_9csamtools_IteratorSNPCalls *__pyx_vtabptr_9csamtools_IteratorSNPCalls;
-
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#define __Pyx_TraceDeclarations \
static PyCodeObject *__pyx_frame_code = NULL; \
CYTHON_FRAME_MODIFIER PyFrameObject *__pyx_frame = NULL; \
- int __Pyx_use_tracing = 0;
+ int __Pyx_use_tracing = 0;
#define __Pyx_TraceCall(funcname, srcfile, firstlineno) \
if (unlikely(PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc)) { \
#else
#define __Pyx_TraceDeclarations
- #define __Pyx_TraceCall(funcname, srcfile, firstlineno)
- #define __Pyx_TraceException()
- #define __Pyx_TraceReturn(result)
+ #define __Pyx_TraceCall(funcname, srcfile, firstlineno)
+ #define __Pyx_TraceException()
+ #define __Pyx_TraceReturn(result)
#endif /* CYTHON_PROFILE */
static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict,
const char* function_name, int kw_allowed); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+
static void __Pyx_RaiseDoubleKeywordsError(
const char* func_name, PyObject* kw_name); /*proto*/
-static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
- Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
-
static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
+ Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
const char *name, int exact); /*proto*/
return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
}
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
-
static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
if (likely(PyList_CheckExact(L))) {
if (PyList_Append(L, x) < 0) return NULL;
static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
-
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
-static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, const char *modname); /*proto*/
+static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
+ PyObject *modname); /*proto*/
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+#define __pyx_binding_PyCFunctionType_USED 1
+
+typedef struct {
+ PyCFunctionObject func;
+} __pyx_binding_PyCFunctionType_object;
+
+static PyTypeObject __pyx_binding_PyCFunctionType_type;
+static PyTypeObject *__pyx_binding_PyCFunctionType = NULL;
+
+static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module); /* proto */
+#define __pyx_binding_PyCFunctionType_New(ml, self) __pyx_binding_PyCFunctionType_NewEx(ml, self, NULL)
+
+static int __pyx_binding_PyCFunctionType_init(void); /* proto */
+
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint8_t(uint8_t);
-static int __Pyx_Print(PyObject*, PyObject *, int); /*proto*/
-#if PY_MAJOR_VERSION >= 3
-static PyObject* __pyx_print = 0;
-static PyObject* __pyx_print_kwargs = 0;
-#endif
-
-static int __Pyx_PrintOne(PyObject* stream, PyObject *o); /*proto*/
-
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint64_t(uint64_t);
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
/* Module declarations from cpython.float */
+/* Module declarations from __builtin__ */
+
/* Module declarations from cpython.complex */
+static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
/* Module declarations from cpython.string */
/* Module declarations from cpython.unicode */
static PyTypeObject *__pyx_ptype_9csamtools_file = 0;
static PyTypeObject *__pyx_ptype_9csamtools_AlignedRead = 0;
static PyTypeObject *__pyx_ptype_9csamtools_Samfile = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorRow = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAll = 0;
static PyTypeObject *__pyx_ptype_9csamtools_PileupProxy = 0;
static PyTypeObject *__pyx_ptype_9csamtools_PileupRead = 0;
static PyTypeObject *__pyx_ptype_9csamtools_Fastafile = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorRow = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowRegion = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAll = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAllRefs = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowSelection = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumn = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnRegion = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnAllRefs = 0;
static PyTypeObject *__pyx_ptype_9csamtools_SNPCall = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_SNPCallerBase = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorSNPCalls = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_SNPCaller = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IndelCall = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IndelCallerBase = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IndelCaller = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorIndelCalls = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IndexedReads = 0;
static char *__pyx_v_9csamtools_bam_nt16_rev_table;
static int __pyx_v_9csamtools_max_pos;
static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *, uint32_t, uint32_t); /*proto*/
static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *, uint32_t, uint32_t); /*proto*/
#define __Pyx_MODULE_NAME "csamtools"
-int __pyx_module_is_main_csamtools = 0;
+static int __pyx_module_is_main_csamtools = 0;
/* Implementation of csamtools */
static PyObject *__pyx_builtin_open;
static PyObject *__pyx_builtin_IOError;
static PyObject *__pyx_builtin_OverflowError;
static PyObject *__pyx_builtin_NotImplementedError;
+static PyObject *__pyx_builtin_OSError;
+static PyObject *__pyx_builtin_AttributeError;
static PyObject *__pyx_builtin_KeyError;
static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_cmp;
static PyObject *__pyx_builtin_chr;
static PyObject *__pyx_builtin_TypeError;
-static PyObject *__pyx_builtin_range;
static char __pyx_k_1[] = "\t";
static char __pyx_k_2[] = "\n";
static char __pyx_k_3[] = "calling len() on closed file";
-static char __pyx_k_4[] = "could not open file `%s`";
-static char __pyx_k_5[] = "I/O operation on closed file";
-static char __pyx_k_6[] = "no sequence/region supplied.";
-static char __pyx_k_7[] = "invalid region: start (%i) > end (%i)";
-static char __pyx_k_8[] = "";
-static char __pyx_k_9[] = "start out of range (%i)";
-static char __pyx_k_10[] = "end out of range (%i)";
-static char __pyx_k_11[] = "%s:%i-%i";
-static char __pyx_k_12[] = "invalid file opening mode `%s`";
-static char __pyx_k_13[] = "http:";
-static char __pyx_k_14[] = "ftp:";
-static char __pyx_k_15[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing";
-static char __pyx_k_16[] = "unequal names and lengths of reference sequences";
-static char __pyx_k_17[] = "-";
-static char __pyx_k_18[] = "file `%s` not found";
-static char __pyx_k_19[] = "could not open file (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_20[] = "file does not have valid header (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_21[] = "file header is empty (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_22[] = ".bai";
-static char __pyx_k_23[] = "error while opening index `%s` ";
-static char __pyx_k_24[] = "tid %i out of range 0<=tid<%i";
-static char __pyx_k_25[] = "[:-]";
-static char __pyx_k_26[] = "invalid reference `%s`";
-static char __pyx_k_27[] = "invalid coordinates: start (%i) > end (%i)";
-static char __pyx_k_28[] = "seek only available in bam files";
-static char __pyx_k_30[] = "fetch called on bamfile without index";
-static char __pyx_k_31[] = "callback functionality requires a region/reference";
-static char __pyx_k_32[] = "no index available for fetch";
-static char __pyx_k_33[] = "fetch called for samfile without header";
-static char __pyx_k_34[] = "fetch for a region is not available for sam files";
-static char __pyx_k_35[] = "callback not implemented yet";
-static char __pyx_k_36[] = "read %s: is unpaired";
-static char __pyx_k_37[] = "mate %s: is unmapped";
-static char __pyx_k_38[] = "mate not found";
-static char __pyx_k_40[] = "counting functionality requires a region/reference";
-static char __pyx_k_41[] = "count for a region is not available for sam files";
-static char __pyx_k_42[] = "no index available for pileup";
-static char __pyx_k_43[] = "pileup of samfiles not implemented yet";
-static char __pyx_k_44[] = "@";
-static char __pyx_k_45[] = "header line without '@': '%s'";
-static char __pyx_k_46[] = "header line with invalid type '%s': '%s'";
-static char __pyx_k_47[] = ":";
-static char __pyx_k_48[] = "unknown field code '%s' in record '%s'";
-static char __pyx_k_49[] = "multiple '%s' lines are not permitted";
-static char __pyx_k_50[] = "@%s";
-static char __pyx_k_51[] = "%s:%s";
-static char __pyx_k_52[] = "invalid type for record %s: %s, expected %s";
-static char __pyx_k_53[] = "incomplete sequence information in '%s'";
-static char __pyx_k_54[] = "no index available for iteration";
-static char __pyx_k_55[] = "can only use this iterator on bam files";
-static char __pyx_k_56[] = "reference sequence for '%s' (tid=%i) not found";
-static char __pyx_k_57[] = "unknown stepper option `%s` in IteratorColumn";
-static char __pyx_k_59[] = "error during iteration";
-static char __pyx_k_60[] = "Invalid clipping in CIGAR string";
-static char __pyx_k_61[] = "quality and sequence mismatch: %i != %i";
-static char __pyx_k_62[] = "%c";
-static char __pyx_k_63[] = "create_string_buffer";
-static char __pyx_k_64[] = "<cccf";
-static char __pyx_k_65[] = "<cccb";
-static char __pyx_k_66[] = "<ccch";
-static char __pyx_k_67[] = "integer %i out of range of BAM/SAM specification";
-static char __pyx_k_68[] = "<ccci";
-static char __pyx_k_69[] = "<cccB";
-static char __pyx_k_70[] = "<cccH";
-static char __pyx_k_71[] = "<cccI";
-static char __pyx_k_72[] = "<cccc";
-static char __pyx_k_73[] = "<ccc%is";
-static char __pyx_k_74[] = "tags field too large";
-static char __pyx_k_75[] = "tag '%s' not present";
-static char __pyx_k_76[] = "Contig index";
-static char __pyx_k_77[] = "Mapped position on contig";
-static char __pyx_k_78[] = "Contig index for mate pair";
-static char __pyx_k_79[] = "Position of mate pair";
-static char __pyx_k_80[] = "Insert size";
-static char __pyx_k_81[] = "Binary flag";
-static char __pyx_k_82[] = "Count of cigar entries";
-static char __pyx_k_83[] = "Cigar entries";
-static char __pyx_k_84[] = "Mapping quality";
-static char __pyx_k_85[] = "Bam index bin number";
-static char __pyx_k_86[] = "Length of query name";
-static char __pyx_k_87[] = "Query name";
-static char __pyx_k_88[] = "Length of query sequence";
-static char __pyx_k_89[] = "Query sequence";
-static char __pyx_k_90[] = "Quality scores";
-static char __pyx_k_91[] = "Length of auxilary data";
-static char __pyx_k_92[] = "Maximum data length";
-static char __pyx_k_93[] = "Current data length";
-static char __pyx_k_94[] = "%-30s %-10s= %s";
-static char __pyx_k_95[] = "(";
-static char __pyx_k_96[] = ")";
-static char __pyx_k_97[] = "This class cannot be instantiated from Python";
+static char __pyx_k_5[] = "could not open file `%s`";
+static char __pyx_k_6[] = "I/O operation on closed file";
+static char __pyx_k_9[] = "no sequence/region supplied.";
+static char __pyx_k_11[] = "invalid region: start (%i) > end (%i)";
+static char __pyx_k_12[] = "";
+static char __pyx_k_13[] = "start out of range (%i)";
+static char __pyx_k_14[] = "end out of range (%i)";
+static char __pyx_k_15[] = "%s:%i-%i";
+static char __pyx_k_17[] = "invalid file opening mode `%s`";
+static char __pyx_k_18[] = "-";
+static char __pyx_k_19[] = "http:";
+static char __pyx_k_20[] = "ftp:";
+static char __pyx_k_21[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing";
+static char __pyx_k_22[] = "unequal names and lengths of reference sequences";
+static char __pyx_k_23[] = "@SQ\tSN:%s\tLN:%s\n";
+static char __pyx_k_24[] = "file `%s` not found";
+static char __pyx_k_25[] = "could not open file (mode='%s') - is it SAM/BAM format?";
+static char __pyx_k_26[] = "file does not have valid header (mode='%s') - is it SAM/BAM format?";
+static char __pyx_k_27[] = ".bai";
+static char __pyx_k_28[] = "error while opening index `%s` ";
+static char __pyx_k_31[] = "tid %i out of range 0<=tid<%i";
+static char __pyx_k_33[] = "[:-]";
+static char __pyx_k_35[] = "invalid reference `%s`";
+static char __pyx_k_36[] = "invalid coordinates: start (%i) > end (%i)";
+static char __pyx_k_38[] = "seek only available in bam files";
+static char __pyx_k_40[] = "seek no available in streams";
+static char __pyx_k_46[] = "fetch called on bamfile without index";
+static char __pyx_k_48[] = "callback functionality requires a region/reference";
+static char __pyx_k_50[] = "no index available for fetch";
+static char __pyx_k_52[] = "fetching by region is not available for sam files";
+static char __pyx_k_54[] = "fetch called for samfile without header";
+static char __pyx_k_56[] = "callback not implemented yet";
+static char __pyx_k_58[] = "read %s: is unpaired";
+static char __pyx_k_59[] = "mate %s: is unmapped";
+static char __pyx_k_60[] = "mate not found";
+static char __pyx_k_65[] = "counting functionality requires a region/reference";
+static char __pyx_k_68[] = "count for a region is not available for sam files";
+static char __pyx_k_71[] = "no index available for pileup";
+static char __pyx_k_74[] = "pileup of samfiles not implemented yet";
+static char __pyx_k_81[] = "Samfile.mapped only available in bam files";
+static char __pyx_k_84[] = "Samfile.unmapped only available in bam files";
+static char __pyx_k_89[] = "@";
+static char __pyx_k_91[] = "header line without '@': '%s'";
+static char __pyx_k_93[] = "header line with invalid type '%s': '%s'";
+static char __pyx_k_94[] = ":";
+static char __pyx_k_96[] = "unknown field code '%s' in record '%s'";
+static char __pyx_k_97[] = "multiple '%s' lines are not permitted";
+static char __pyx_k_98[] = "@%s";
+static char __pyx_k_99[] = "%s:%s";
static char __pyx_k__A[] = "A";
static char __pyx_k__C[] = "C";
static char __pyx_k__D[] = "D";
static char __pyx_k__s[] = "s";
static char __pyx_k__w[] = "w";
static char __pyx_k__x[] = "x";
-static char __pyx_k_100[] = "No such file or directory: '%s'";
-static char __pyx_k_101[] = "-o";
-static char __pyx_k_102[] = "option -o is forbidden in samtools view";
-static char __pyx_k_103[] = "_rms_mapping_quality";
-static char __pyx_k_104[] = "--> read %i %s %i";
-static char __pyx_k_105[] = "pos=%i, cns=%i, q_r = %f, depth=%i, n=%i, rb=%i, cns-cq=%i %i %i %i";
-static char __pyx_k_106[] = "-------------------------------------\n";
-static char __pyx_k_107[] = "IteratorSNPCalls requires an pileup iterator with reference sequence";
-static char __pyx_k_108[] = "position %i out of bounds on reference sequence (len=%i)";
-static char __pyx_k_109[] = "no reads in region - no call";
-static char __pyx_k_110[] = "%s/%s";
-static char __pyx_k_111[] = "IndelCallerBase requires an pileup iterator with reference sequence";
-static char __pyx_k_112[] = "can only IndexReads on bam files";
-static char __pyx_k_113[] = "read %s not found";
-static char __pyx_k_114[] = "the query name (None if not present)";
-static char __pyx_k_115[] = "the :term:`cigar` alignment (None if not present).\n ";
-static char __pyx_k_116[] = "read sequence bases, including :term:`soft clipped` bases (None if not present)";
-static char __pyx_k_117[] = "read sequence base qualities, including :term:`soft clipped` bases (None if not present)";
-static char __pyx_k_118[] = "aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present)\n\n SAM/BAM files may included extra flanking bases sequences that were\n not part of the alignment. These bases may be the result of the\n Smith-Waterman or other algorithms, which may not require alignments\n that begin at the first residue or end at the last. In addition,\n extra sequencing adapters, multiplex identifiers, and low-quality bases that\n were not considered for alignment may have been retained.";
-static char __pyx_k_119[] = "aligned query sequence quality values (None if not present)";
-static char __pyx_k_120[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
-static char __pyx_k_121[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
-static char __pyx_k_122[] = "Length of the aligned query sequence";
-static char __pyx_k_123[] = "the tags in the AUX field.\n\n This property permits convenience access to \n the tags. Changes it the returned list will\n not update the tags automatically. Instead,\n the following is required for adding a \n new tag::\n\n read.tags = read.tags + [(\"RG\",0)]\n\n ";
-static char __pyx_k_124[] = "properties flag";
-static char __pyx_k_125[] = "\n :term:`target` ID\n\n DEPRECATED from pysam-0.4 - use tid in the future.\n The rname field caused a lot of confusion as it returns\n the :term:`target` ID instead of the reference sequence\n name.\n\n .. note::\n\n This field contains the index of the reference sequence \n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n \n ";
-static char __pyx_k_126[] = "\n :term:`target` ID\n\n .. note::\n\n This field contains the index of the reference sequence \n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n \n ";
-static char __pyx_k_127[] = "0-based leftmost coordinate";
-static char __pyx_k_128[] = "properties bin";
-static char __pyx_k_129[] = "length of the read (read only). Returns 0 if not given.";
-static char __pyx_k_130[] = "aligned end position of the read (read only). Returns\n None if not available.";
-static char __pyx_k_131[] = "aligned length of the read (read only). Returns None if\n not available.";
-static char __pyx_k_132[] = "mapping quality";
-static char __pyx_k_133[] = "the :term:`reference` id of the mate ";
-static char __pyx_k_134[] = "the position of the mate";
-static char __pyx_k_135[] = "the insert size";
-static char __pyx_k_136[] = "true if read is paired in sequencing";
-static char __pyx_k_137[] = "true if read is mapped in a proper pair";
-static char __pyx_k_138[] = "true if read itself is unmapped";
-static char __pyx_k_139[] = "true if the mate is unmapped";
-static char __pyx_k_140[] = "true if read is mapped to reverse strand";
-static char __pyx_k_141[] = "true is read is mapped to reverse strand";
-static char __pyx_k_142[] = "true if this is read1";
-static char __pyx_k_143[] = "true if this is read2";
-static char __pyx_k_144[] = "true if not primary alignment";
-static char __pyx_k_145[] = "true if QC failure";
-static char __pyx_k_146[] = "true if optical or PCR duplicate";
-static char __pyx_k_147[] = "a list of reference positions that this read aligns to.";
-static char __pyx_k_148[] = "number of :term:`filename` associated with this object.";
-static char __pyx_k_149[] = "number of :term:`reference` sequences in the file.";
-static char __pyx_k_150[] = "tuple with the names of :term:`reference` sequences.";
-static char __pyx_k_151[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as \n :attr:`pysam.Samfile.references`\n ";
-static char __pyx_k_152[] = "full contents of the :term:`sam file` header as a string.";
-static char __pyx_k_153[] = "header information within the :term:`sam file`. The records and fields are returned as \n a two-level dictionary.\n ";
-static char __pyx_k_154[] = "the chromosome ID as is defined in the header";
-static char __pyx_k_155[] = "number of reads mapping to this column.";
-static char __pyx_k_156[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
-static char __pyx_k_157[] = "a :class:`pysam.AlignedRead` object of the aligned read";
-static char __pyx_k_158[] = "position of the read base at the pileup site, 0-based";
-static char __pyx_k_159[] = "indel length; 0 for no indel, positive for ins and negative for del";
-static char __pyx_k_160[] = "1 iff the base on the padded read is a deletion";
-static char __pyx_k_161[] = "current sequence length.";
-static char __pyx_k_162[] = "nucleotide position of SNP.";
-static char __pyx_k_163[] = "reference base at pos. ``N`` if no reference sequence supplied.";
-static char __pyx_k_164[] = "the genotype called.";
-static char __pyx_k_165[] = "the genotype quality (Phred-scaled).";
-static char __pyx_k_166[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
-static char __pyx_k_167[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
-static char __pyx_k_168[] = "coverage or read depth - the number of reads involved in the call.";
-static char __pyx_k_169[] = "sequence of first allele.";
-static char __pyx_k_170[] = "sequence of second allele.";
-static char __pyx_k_171[] = "reads supporting first allele.";
-static char __pyx_k_172[] = "=ACMGRSVTWYHKDBN";
-static char __pyx_k_173[] = "A pileup column. A pileup column contains \n all the reads that map to a certain target base.\n\n tid \n chromosome ID as is defined in the header \n pos \n the target base coordinate (0-based) \n n \n number of reads mapping to this column \n pileups \n list of reads (:class:`pysam.PileupRead`) aligned to this column \n ";
-static char __pyx_k_174[] = "\n stderr is captured. \n ";
-static char __pyx_k_175[] = "does nothing. stderr can't be redirected on windows";
-static char __pyx_k_176[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
-static char __pyx_k_177[] = "Fastafile._isOpen (line 265)";
-static char __pyx_k_178[] = "Fastafile._open (line 275)";
-static char __pyx_k_179[] = "Fastafile.fetch (line 306)";
-static char __pyx_k_180[] = "Samfile._isOpen (line 464)";
-static char __pyx_k_181[] = "Samfile._hasIndex (line 468)";
-static char __pyx_k_182[] = "Samfile._open (line 472)";
-static char __pyx_k_183[] = "Samfile.gettid (line 612)";
-static char __pyx_k_184[] = "Samfile.getrname (line 621)";
-static char __pyx_k_185[] = "Samfile._parseRegion (line 637)";
-static char __pyx_k_186[] = "Samfile.seek (line 691)";
-static char __pyx_k_187[] = "Samfile.tell (line 702)";
-static char __pyx_k_188[] = "Samfile.fetch (line 713)";
-static char __pyx_k_189[] = "Samfile.mate (line 782)";
-static char __pyx_k_190[] = "Samfile.count (line 825)";
-static char __pyx_k_191[] = "Samfile.pileup (line 869)";
-static char __pyx_k_192[] = "Samfile.close (line 953)";
-static char __pyx_k_193[] = "Samfile.write (line 969)";
-static char __pyx_k_194[] = "Samfile._buildLine (line 1078)";
-static char __pyx_k_195[] = "Samfile.__next__ (line 1173)";
-static char __pyx_k_196[] = "IteratorRowRegion.__next__ (line 1281)";
-static char __pyx_k_197[] = "IteratorRowAll.__next__ (line 1340)";
-static char __pyx_k_198[] = "IteratorRowAllRefs.__next__ (line 1375)";
-static char __pyx_k_199[] = "IteratorRowSelection.__next__ (line 1459)";
-static char __pyx_k_200[] = "IteratorRowSelection";
-static char __pyx_k_201[] = "IteratorColumn.addReference (line 1634)";
-static char __pyx_k_202[] = "IteratorColumn.hasReference (line 1642)";
-static char __pyx_k_203[] = "IteratorColumnRegion.__next__ (line 1724)";
-static char __pyx_k_204[] = "IteratorColumnRegion";
-static char __pyx_k_205[] = "IteratorColumnAllRefs.__next__ (line 1755)";
-static char __pyx_k_206[] = "IteratorColumnAllRefs";
-static char __pyx_k_207[] = "AlignedRead.__str__ (line 1903)";
-static char __pyx_k_208[] = "AlignedRead.compare (line 1928)";
-static char __pyx_k_209[] = "AlignedRead.overlap (line 2512)";
-static char __pyx_k_210[] = "AlignedRead.opt (line 2541)";
-static char __pyx_k_211[] = "AlignedRead.fancy_str (line 2563)";
-static char __pyx_k_212[] = "Outs.setdevice (line 2705)";
-static char __pyx_k_213[] = "Outs.setfile (line 2710)";
-static char __pyx_k_214[] = "Outs.restore (line 2723)";
-static char __pyx_k_215[] = "_samtools_dispatch (line 2734)";
-static char __pyx_k_216[] = "IteratorSNPCalls.__next__ (line 2969)";
-static char __pyx_k_217[] = "SNPCaller.call (line 3041)";
-static char __pyx_k_218[] = "IndelCaller.call (line 3306)";
-static char __pyx_k_219[] = "IteratorIndelCalls.__next__ (line 3353)";
-static char __pyx_k_220[] = "IndexedReads.build (line 3406)";
+static char __pyx_k_100[] = "invalid type for record %s: %s, expected %s";
+static char __pyx_k_101[] = "incomplete sequence information in '%s'";
+static char __pyx_k_103[] = "can not iterate over samfile without header";
+static char __pyx_k_106[] = "no index available for iteration";
+static char __pyx_k_112[] = "can only use this iterator on bam files";
+static char __pyx_k_113[] = "reference sequence for '%s' (tid=%i) not found";
+static char __pyx_k_114[] = "unknown stepper option `%s` in IteratorColumn";
+static char __pyx_k_116[] = "error during iteration";
+static char __pyx_k_119[] = "Invalid clipping in CIGAR string";
+static char __pyx_k_120[] = "quality and sequence mismatch: %i != %i";
+static char __pyx_k_121[] = "%c";
+static char __pyx_k_122[] = "create_string_buffer";
+static char __pyx_k_123[] = "<cccf";
+static char __pyx_k_124[] = "<cccb";
+static char __pyx_k_125[] = "<ccch";
+static char __pyx_k_126[] = "integer %i out of range of BAM/SAM specification";
+static char __pyx_k_127[] = "<ccci";
+static char __pyx_k_128[] = "<cccB";
+static char __pyx_k_129[] = "<cccH";
+static char __pyx_k_130[] = "<cccI";
+static char __pyx_k_131[] = "<cccc";
+static char __pyx_k_132[] = "<ccc%is";
+static char __pyx_k_133[] = "tags field too large";
+static char __pyx_k_135[] = "tag '%s' not present";
+static char __pyx_k_136[] = "Contig index";
+static char __pyx_k_137[] = "Mapped position on contig";
+static char __pyx_k_138[] = "Contig index for mate pair";
+static char __pyx_k_139[] = "Position of mate pair";
+static char __pyx_k_140[] = "Insert size";
+static char __pyx_k_141[] = "Binary flag";
+static char __pyx_k_142[] = "Count of cigar entries";
+static char __pyx_k_143[] = "Cigar entries";
+static char __pyx_k_144[] = "Mapping quality";
+static char __pyx_k_145[] = "Bam index bin number";
+static char __pyx_k_146[] = "Length of query name";
+static char __pyx_k_147[] = "Query name";
+static char __pyx_k_148[] = "Length of query sequence";
+static char __pyx_k_149[] = "Query sequence";
+static char __pyx_k_150[] = "Quality scores";
+static char __pyx_k_151[] = "Length of auxilary data";
+static char __pyx_k_152[] = "Maximum data length";
+static char __pyx_k_153[] = "Current data length";
+static char __pyx_k_154[] = "%-30s %-10s= %s";
+static char __pyx_k_155[] = "(";
+static char __pyx_k_156[] = ")";
+static char __pyx_k_157[] = "This class cannot be instantiated from Python";
+static char __pyx_k_162[] = "No such file or directory: '%s'";
+static char __pyx_k_163[] = "-o";
+static char __pyx_k_164[] = "option -o is forbidden in samtools view";
+static char __pyx_k_166[] = "_rms_mapping_quality";
+static char __pyx_k_167[] = "can only IndexReads on bam files";
+static char __pyx_k_168[] = "read %s not found";
+static char __pyx_k_169[] = "the query name (None if not present)";
+static char __pyx_k_170[] = "the :term:`cigar` alignment (None if not present).\n ";
+static char __pyx_k_171[] = "read sequence bases, including :term:`soft clipped` bases (None if not present)";
+static char __pyx_k_172[] = "read sequence base qualities, including :term:`soft clipped` bases (None if not present)";
+static char __pyx_k_173[] = "aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present)\n\n SAM/BAM files may included extra flanking bases sequences that were\n not part of the alignment. These bases may be the result of the\n Smith-Waterman or other algorithms, which may not require alignments\n that begin at the first residue or end at the last. In addition,\n extra sequencing adapters, multiplex identifiers, and low-quality bases that\n were not considered for alignment may have been retained.";
+static char __pyx_k_174[] = "aligned query sequence quality values (None if not present)";
+static char __pyx_k_175[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
+static char __pyx_k_176[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
+static char __pyx_k_177[] = "Length of the aligned query sequence";
+static char __pyx_k_178[] = "the tags in the AUX field.\n\n This property permits convenience access to \n the tags. Changes it the returned list will\n not update the tags automatically. Instead,\n the following is required for adding a \n new tag::\n\n read.tags = read.tags + [(\"RG\",0)]\n\n\n This method will happily write the same tag\n multiple times.\n ";
+static char __pyx_k_179[] = "properties flag";
+static char __pyx_k_180[] = "\n :term:`target` ID\n\n DEPRECATED from pysam-0.4 - use tid in the future.\n The rname field caused a lot of confusion as it returns\n the :term:`target` ID instead of the reference sequence\n name.\n\n .. note::\n\n This field contains the index of the reference sequence \n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n \n ";
+static char __pyx_k_181[] = "\n :term:`target` ID\n\n .. note::\n\n This field contains the index of the reference sequence \n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n \n ";
+static char __pyx_k_182[] = "0-based leftmost coordinate";
+static char __pyx_k_183[] = "properties bin";
+static char __pyx_k_184[] = "length of the read (read only). Returns 0 if not given.";
+static char __pyx_k_185[] = "aligned end position of the read on the reference genome. Returns\n None if not available.";
+static char __pyx_k_186[] = "aligned length of the read on the reference genome. Returns None if\n not available.";
+static char __pyx_k_187[] = "mapping quality";
+static char __pyx_k_188[] = "the :term:`reference` id of the mate \n deprecated, use RNEXT instead.\n ";
+static char __pyx_k_189[] = "the :term:`reference` id of the mate ";
+static char __pyx_k_190[] = "the position of the mate\n deprecated, use PNEXT instead.";
+static char __pyx_k_191[] = "the position of the mate";
+static char __pyx_k_192[] = "the insert size\n deprecated: use tlen instead";
+static char __pyx_k_193[] = "the insert size";
+static char __pyx_k_194[] = "true if read is paired in sequencing";
+static char __pyx_k_195[] = "true if read is mapped in a proper pair";
+static char __pyx_k_196[] = "true if read itself is unmapped";
+static char __pyx_k_197[] = "true if the mate is unmapped";
+static char __pyx_k_198[] = "true if read is mapped to reverse strand";
+static char __pyx_k_199[] = "true is read is mapped to reverse strand";
+static char __pyx_k_200[] = "true if this is read1";
+static char __pyx_k_201[] = "true if this is read2";
+static char __pyx_k_202[] = "true if not primary alignment";
+static char __pyx_k_203[] = "true if QC failure";
+static char __pyx_k_204[] = "true if optical or PCR duplicate";
+static char __pyx_k_205[] = "a list of reference positions that this read aligns to.";
+static char __pyx_k_206[] = "number of :term:`filename` associated with this object.";
+static char __pyx_k_207[] = "number of :term:`reference` sequences in the file.";
+static char __pyx_k_208[] = "tuple with the names of :term:`reference` sequences.";
+static char __pyx_k_209[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as \n :attr:`pysam.Samfile.references`\n ";
+static char __pyx_k_210[] = "total number of mapped reads in file.\n ";
+static char __pyx_k_211[] = "total number of unmapped reads in file.\n ";
+static char __pyx_k_212[] = "full contents of the :term:`sam file` header as a string.";
+static char __pyx_k_213[] = "header information within the :term:`sam file`. The records and fields are returned as \n a two-level dictionary.\n ";
+static char __pyx_k_214[] = "the chromosome ID as is defined in the header";
+static char __pyx_k_215[] = "number of reads mapping to this column.";
+static char __pyx_k_216[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
+static char __pyx_k_217[] = "a :class:`pysam.AlignedRead` object of the aligned read";
+static char __pyx_k_218[] = "position of the read base at the pileup site, 0-based";
+static char __pyx_k_219[] = "indel length; 0 for no indel, positive for ins and negative for del";
+static char __pyx_k_220[] = "1 iff the base on the padded read is a deletion";
+static char __pyx_k_221[] = "current sequence length.";
+static char __pyx_k_222[] = "nucleotide position of SNP.";
+static char __pyx_k_223[] = "reference base at pos. ``N`` if no reference sequence supplied.";
+static char __pyx_k_224[] = "the genotype called.";
+static char __pyx_k_225[] = "the genotype quality (Phred-scaled).";
+static char __pyx_k_226[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
+static char __pyx_k_227[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
+static char __pyx_k_228[] = "coverage or read depth - the number of reads involved in the call.";
+static char __pyx_k_229[] = "=ACMGRSVTWYHKDBN";
+static char __pyx_k_230[] = "A pileup column. A pileup column contains \n all the reads that map to a certain target base.\n\n tid \n chromosome ID as is defined in the header \n pos \n the target base coordinate (0-based) \n n \n number of reads mapping to this column \n pileups \n list of reads (:class:`pysam.PileupRead`) aligned to this column \n ";
+static char __pyx_k_231[] = "\n stderr is captured. \n ";
+static char __pyx_k_232[] = "does nothing. stderr can't be redirected on windows";
+static char __pyx_k_238[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
static char __pyx_k__AS[] = "AS";
static char __pyx_k__CL[] = "CL";
static char __pyx_k__CN[] = "CN";
static char __pyx_k__SQ[] = "SQ";
static char __pyx_k__UR[] = "UR";
static char __pyx_k__VN[] = "VN";
-static char __pyx_k___r[] = "_r";
static char __pyx_k__fd[] = "fd";
static char __pyx_k__fp[] = "fp";
static char __pyx_k__id[] = "id";
static char __pyx_k__os[] = "os";
+static char __pyx_k__rU[] = "rU";
static char __pyx_k__rb[] = "rb";
static char __pyx_k__re[] = "re";
static char __pyx_k__wb[] = "wb";
static char __pyx_k__dup[] = "dup";
static char __pyx_k__end[] = "end";
static char __pyx_k__map[] = "map";
-static char __pyx_k__opt[] = "opt";
static char __pyx_k__plp[] = "plp";
static char __pyx_k__pos[] = "pos";
-static char __pyx_k__q_r[] = "q_r";
static char __pyx_k__raw[] = "raw";
static char __pyx_k__seq[] = "seq";
static char __pyx_k__sys[] = "sys";
static char __pyx_k___pos[] = "_pos";
static char __pyx_k___tid[] = "_tid";
static char __pyx_k__args[] = "args";
-static char __pyx_k__call[] = "call";
-static char __pyx_k__cnt1[] = "cnt1";
-static char __pyx_k__cnt2[] = "cnt2";
static char __pyx_k__core[] = "core";
static char __pyx_k__data[] = "data";
static char __pyx_k__dup2[] = "dup2";
static char __pyx_k__seek[] = "seek";
static char __pyx_k__self[] = "self";
static char __pyx_k__tags[] = "tags";
-static char __pyx_k__tell[] = "tell";
static char __pyx_k__text[] = "text";
static char __pyx_k__view[] = "view";
-static char __pyx_k___call[] = "_call";
static char __pyx_k___open[] = "_open";
static char __pyx_k___qpos[] = "_qpos";
static char __pyx_k__bqual[] = "bqual";
-static char __pyx_k__build[] = "build";
static char __pyx_k__cigar[] = "cigar";
static char __pyx_k__close[] = "close";
static char __pyx_k__cnext[] = "cnext";
-static char __pyx_k__count[] = "count";
-static char __pyx_k__fetch[] = "fetch";
static char __pyx_k__flush[] = "flush";
static char __pyx_k__indel[] = "indel";
static char __pyx_k__index[] = "index";
static char __pyx_k__isize[] = "isize";
static char __pyx_k__l_aux[] = "l_aux";
static char __pyx_k__level[] = "level";
-static char __pyx_k__n_hap[] = "n_hap";
static char __pyx_k__n_plp[] = "n_plp";
-static char __pyx_k__q_cns[] = "q_cns";
-static char __pyx_k__q_ref[] = "q_ref";
static char __pyx_k__qname[] = "qname";
-static char __pyx_k__range[] = "range";
-static char __pyx_k__reset[] = "reset";
static char __pyx_k__rname[] = "rname";
static char __pyx_k__setfd[] = "setfd";
static char __pyx_k__split[] = "split";
static char __pyx_k__start[] = "start";
static char __pyx_k__strip[] = "strip";
-static char __pyx_k__theta[] = "theta";
static char __pyx_k__types[] = "types";
static char __pyx_k__where[] = "where";
static char __pyx_k__write[] = "write";
static char __pyx_k___indel[] = "_indel";
static char __pyx_k___level[] = "_level";
+static char __pyx_k__append[] = "append";
static char __pyx_k__ctypes[] = "ctypes";
-static char __pyx_k__errmod[] = "errmod";
static char __pyx_k__exists[] = "exists";
static char __pyx_k__fields[] = "fields";
static char __pyx_k__fileno[] = "fileno";
static char __pyx_k__gettid[] = "gettid";
static char __pyx_k__header[] = "header";
-static char __pyx_k__indel1[] = "indel1";
-static char __pyx_k__indel2[] = "indel2";
static char __pyx_k__is_del[] = "is_del";
static char __pyx_k__l_qseq[] = "l_qseq";
static char __pyx_k__l_text[] = "l_text";
static char __pyx_k__method[] = "method";
static char __pyx_k__object[] = "object";
static char __pyx_k__offset[] = "offset";
-static char __pyx_k__pileup[] = "pileup";
static char __pyx_k__record[] = "record";
static char __pyx_k__region[] = "region";
static char __pyx_k__remove[] = "remove";
static char __pyx_k__system[] = "system";
static char __pyx_k__IOError[] = "IOError";
static char __pyx_k__IntType[] = "IntType";
+static char __pyx_k__OSError[] = "OSError";
static char __pyx_k__O_CREAT[] = "O_CREAT";
static char __pyx_k__Samfile[] = "Samfile";
static char __pyx_k__Windows[] = "Windows";
static char __pyx_k____str__[] = "__str__";
static char __pyx_k___isOpen[] = "_isOpen";
static char __pyx_k___is_del[] = "_is_del";
-static char __pyx_k__compare[] = "compare";
static char __pyx_k__devnull[] = "devnull";
static char __pyx_k__is_head[] = "is_head";
static char __pyx_k__is_tail[] = "is_tail";
static char __pyx_k__l_qname[] = "l_qname";
static char __pyx_k__mkstemp[] = "mkstemp";
static char __pyx_k__n_cigar[] = "n_cigar";
-static char __pyx_k__options[] = "options";
-static char __pyx_k__overlap[] = "overlap";
static char __pyx_k__pileups[] = "pileups";
-static char __pyx_k__q_indel[] = "q_indel";
-static char __pyx_k__r_indel[] = "r_indel";
static char __pyx_k__release[] = "release";
static char __pyx_k__restore[] = "restore";
static char __pyx_k__rowiter[] = "rowiter";
static char __pyx_k____dict__[] = "__dict__";
static char __pyx_k____init__[] = "__init__";
static char __pyx_k____main__[] = "__main__";
-static char __pyx_k____next__[] = "__next__";
static char __pyx_k____test__[] = "__test__";
static char __pyx_k___is_head[] = "_is_head";
static char __pyx_k___is_tail[] = "_is_tail";
static char __pyx_k___logfile[] = "_logfile";
static char __pyx_k__calcsize[] = "calcsize";
static char __pyx_k__callback[] = "callback";
-static char __pyx_k__cap_mapQ[] = "cap_mapQ";
-static char __pyx_k__cnt_anti[] = "cnt_anti";
static char __pyx_k__coverage[] = "coverage";
static char __pyx_k__data_len[] = "data_len";
static char __pyx_k__exc_type[] = "exc_type";
static char __pyx_k__filename[] = "filename";
static char __pyx_k__genotype[] = "genotype";
-static char __pyx_k__getrname[] = "getrname";
-static char __pyx_k__het_rate[] = "het_rate";
static char __pyx_k__isremote[] = "isremote";
+static char __pyx_k__isstream[] = "isstream";
static char __pyx_k__iterdata[] = "iterdata";
static char __pyx_k__nextiter[] = "nextiter";
static char __pyx_k__platform[] = "platform";
static char __pyx_k__template[] = "template";
static char __pyx_k__Fastafile[] = "Fastafile";
static char __pyx_k__FloatType[] = "FloatType";
-static char __pyx_k__SNPCaller[] = "SNPCaller";
static char __pyx_k__TypeError[] = "TypeError";
static char __pyx_k___coverage[] = "_coverage";
static char __pyx_k___delegate[] = "_delegate";
static char __pyx_k___genotype[] = "_genotype";
static char __pyx_k___hasIndex[] = "_hasIndex";
static char __pyx_k__alignment[] = "alignment";
+static char __pyx_k__csamtools[] = "csamtools";
static char __pyx_k__exc_value[] = "exc_value";
-static char __pyx_k__fancy_str[] = "fancy_str";
static char __pyx_k__fastafile[] = "fastafile";
static char __pyx_k__itertools[] = "itertools";
static char __pyx_k__max_depth[] = "max_depth";
-static char __pyx_k__min_baseQ[] = "min_baseQ";
static char __pyx_k__n_targets[] = "n_targets";
static char __pyx_k__pack_into[] = "pack_into";
static char __pyx_k__positions[] = "positions";
static char __pyx_k__ValueError[] = "ValueError";
static char __pyx_k___alignment[] = "_alignment";
static char __pyx_k___buildLine[] = "_buildLine";
-static char __pyx_k__reads_diff[] = "reads_diff";
static char __pyx_k__startswith[] = "startswith";
static char __pyx_k__target_len[] = "target_len";
static char __pyx_k__AlignedRead[] = "AlignedRead";
-static char __pyx_k__IndelCaller[] = "IndelCaller";
static char __pyx_k__IteratorRow[] = "IteratorRow";
static char __pyx_k__PileupProxy[] = "PileupProxy";
static char __pyx_k__StderrStore[] = "StderrStore";
+static char __pyx_k__add_sq_text[] = "add_sq_text";
static char __pyx_k__collections[] = "collections";
static char __pyx_k__current_pos[] = "current_pos";
static char __pyx_k__defaultdict[] = "defaultdict";
-static char __pyx_k__getSequence[] = "getSequence";
static char __pyx_k__nreferences[] = "nreferences";
static char __pyx_k__pileup_iter[] = "pileup_iter";
-static char __pyx_k__reads_first[] = "reads_first";
static char __pyx_k__snp_quality[] = "snp_quality";
static char __pyx_k__stderr_save[] = "stderr_save";
static char __pyx_k__target_name[] = "target_name";
static char __pyx_k___buildHeader[] = "_buildHeader";
static char __pyx_k___parseRegion[] = "_parseRegion";
static char __pyx_k___snp_quality[] = "_snp_quality";
-static char __pyx_k__addReference[] = "addReference";
static char __pyx_k__catch_stderr[] = "catch_stderr";
static char __pyx_k__catch_stdout[] = "catch_stdout";
-static char __pyx_k__first_allele[] = "first_allele";
-static char __pyx_k__hasReference[] = "hasReference";
-static char __pyx_k__n_haplotypes[] = "n_haplotypes";
static char __pyx_k__owns_samfile[] = "owns_samfile";
-static char __pyx_k__reads_second[] = "reads_second";
+static char __pyx_k__start_offset[] = "start_offset";
static char __pyx_k__OverflowError[] = "OverflowError";
static char __pyx_k__StopIteration[] = "StopIteration";
static char __pyx_k__VALID_HEADERS[] = "VALID_HEADERS";
-static char __pyx_k__second_allele[] = "second_allele";
+static char __pyx_k__AttributeError[] = "AttributeError";
static char __pyx_k__IteratorColumn[] = "IteratorColumn";
-static char __pyx_k__IteratorRowAll[] = "IteratorRowAll";
static char __pyx_k__readAndRelease[] = "readAndRelease";
static char __pyx_k__reference_base[] = "reference_base";
static char __pyx_k__referencenames[] = "referencenames";
static char __pyx_k___reference_base[] = "_reference_base";
-static char __pyx_k__iterator_column[] = "iterator_column";
static char __pyx_k__mapping_quality[] = "mapping_quality";
-static char __pyx_k__IteratorSNPCalls[] = "IteratorSNPCalls";
static char __pyx_k____getattribute__[] = "__getattribute__";
static char __pyx_k__referencelengths[] = "referencelengths";
-static char __pyx_k__IteratorRowRegion[] = "IteratorRowRegion";
static char __pyx_k__consensus_quality[] = "consensus_quality";
static char __pyx_k__setupIteratorData[] = "setupIteratorData";
-static char __pyx_k__IteratorIndelCalls[] = "IteratorIndelCalls";
-static char __pyx_k__IteratorRowAllRefs[] = "IteratorRowAllRefs";
static char __pyx_k__StderrStoreWindows[] = "StderrStoreWindows";
static char __pyx_k__VALID_HEADER_ORDER[] = "VALID_HEADER_ORDER";
static char __pyx_k__VALID_HEADER_TYPES[] = "VALID_HEADER_TYPES";
static char __pyx_k__NotImplementedError[] = "NotImplementedError";
static char __pyx_k__VALID_HEADER_FIELDS[] = "VALID_HEADER_FIELDS";
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static PyObject *__pyx_n_s__AS;
static PyObject *__pyx_n_s__AlignedRead;
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static PyObject *__pyx_n_s__C;
static PyObject *__pyx_n_s__CL;
static PyObject *__pyx_n_s__CN;
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static PyObject *__pyx_n_s__IndexedReads;
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static PyObject *__pyx_n_s__KeyError;
static PyObject *__pyx_n_s__LB;
static PyObject *__pyx_n_s__LN;
static PyObject *__pyx_n_s__M5;
static PyObject *__pyx_n_s__NotImplementedError;
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static PyObject *__pyx_n_s__O_CREAT;
static PyObject *__pyx_n_s__O_WRONLY;
static PyObject *__pyx_n_s__Outs;
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static PyObject *__pyx_n_s__SM;
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static PyObject *__pyx_n_s___snp_quality;
static PyObject *__pyx_n_s___tid;
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static PyObject *__pyx_n_s__alignment;
static PyObject *__pyx_n_s__all;
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static PyObject *__pyx_n_s__args;
static PyObject *__pyx_n_s__b;
static PyObject *__pyx_n_s__bam;
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static PyObject *__pyx_n_s__collections;
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static PyObject *__pyx_n_s__core;
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static PyObject *__pyx_n_s__coverage;
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static PyObject *__pyx_n_s__ctypes;
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*/
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}
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#endif
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+ &__pyx_tp_as_buffer_AlignedRead, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("AlignedRead()\n\n Class representing an aligned read. see SAM format specification for \n the meaning of fields (http://samtools.sourceforge.net/).\n\n This class stores a handle to the samtools C-structure representing\n an aligned read. Member read access is forwarded to the C-structure\n and converted into python objects. This implementation should be fast,\n as only the data needed is converted.\n\n For write access, the C-structure is updated in-place. This is\n not the most efficient way to build BAM entries, as the variable\n length data is concatenated and thus needs to resized if\n a field is updated. Furthermore, the BAM entry might be\n in an inconsistent state. The :meth:`~validate` method can\n be used to check if an entry is consistent.\n\n One issue to look out for is that the sequence should always\n be set *before* the quality scores. Setting the sequence will\n also erase any quality scores that were set previously.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_14IteratorRowAll___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_14IteratorRowAll___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_AlignedRead, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_9csamtools_AlignedRead, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- 0, /*tp_init*/
+ __pyx_pf_9csamtools_11AlignedRead___init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowAll, /*tp_new*/
+ __pyx_tp_new_9csamtools_AlignedRead, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_9csamtools_Samfile __pyx_vtable_9csamtools_Samfile;
-static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_Samfile *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_Samfile *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_Samfile;
+ if (__pyx_pf_9csamtools_7Samfile___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
- Py_XDECREF(((PyObject *)p->samfile));
- Py_XDECREF(((PyObject *)p->rowiter));
- __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) {
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pf_9csamtools_7Samfile_15__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ (*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
- e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
- }
- if (p->samfile) {
- e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
- }
- if (p->rowiter) {
- e = (*v)(((PyObject*)p->rowiter), a); if (e) return e;
- }
- return 0;
+static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_8filename___get__(o);
}
-static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
- PyObject* tmp;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
- __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
- }
- tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->rowiter);
- p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
+static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_11nreferences___get__(o);
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = {
- {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_nextiter)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs___next__)},
+static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_10references___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_7lengths___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_mapped(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_6mapped___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_unmapped(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_8unmapped___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_text(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_4text___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_header(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_6header___get__(o);
+}
+
+static PyMethodDef __pyx_methods_9csamtools_Samfile[] = {
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_1_isOpen)},
+ {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_2_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_2_hasIndex)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_3_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_3_open)},
+ {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_4gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_4gettid)},
+ {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_5getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_5getrname)},
+ {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_6_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_6_parseRegion)},
+ {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_7reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_7reset)},
+ {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_8seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_8seek)},
+ {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_9tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_9tell)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_10fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_10fetch)},
+ {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_11mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_11mate)},
+ {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_12count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_12count)},
+ {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_13pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_13pileup)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_14close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_14close)},
+ {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_16write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_16write)},
+ {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_17__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_17__enter__)},
+ {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_18__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_18__exit__)},
+ {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_19_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_19_buildLine)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_21__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_21__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = {
+static struct PyGetSetDef __pyx_getsets_9csamtools_Samfile[] = {
+ {(char *)"filename", __pyx_getprop_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_206), 0},
+ {(char *)"nreferences", __pyx_getprop_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_207), 0},
+ {(char *)"references", __pyx_getprop_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_208), 0},
+ {(char *)"lengths", __pyx_getprop_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_209), 0},
+ {(char *)"mapped", __pyx_getprop_9csamtools_7Samfile_mapped, 0, __Pyx_DOCSTR(__pyx_k_210), 0},
+ {(char *)"unmapped", __pyx_getprop_9csamtools_7Samfile_unmapped, 0, __Pyx_DOCSTR(__pyx_k_211), 0},
+ {(char *)"text", __pyx_getprop_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_212), 0},
+ {(char *)"header", __pyx_getprop_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_213), 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_Samfile = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = {
+static PySequenceMethods __pyx_tp_as_sequence_Samfile = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAllRefs = {
+static PyMappingMethods __pyx_tp_as_mapping_Samfile = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = {
+static PyBufferProcs __pyx_tp_as_buffer_Samfile = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
+static PyTypeObject __pyx_type_9csamtools_Samfile = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.Samfile"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_Samfile), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_Samfile, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRowAllRefs, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowAllRefs, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowAllRefs, /*tp_as_mapping*/
+ &__pyx_tp_as_number_Samfile, /*tp_as_number*/
+ &__pyx_tp_as_sequence_Samfile, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_Samfile, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/
+ &__pyx_tp_as_buffer_Samfile, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,\n add_sq_text = False )*\n \n A :term:`SAM`/:term:`BAM` formatted file. The file is automatically opened.\n \n *mode* should be ``r`` for reading or ``w`` for writing. The default is text mode (:term:`SAM`). For binary \n (:term:`BAM`) I/O you should append ``b`` for compressed or ``u`` for uncompressed :term:`BAM` output. \n Use ``h`` to output header information in text (:term:`TAM`) mode.\n\n If ``b`` is present, it must immediately follow ``r`` or ``w``. \n Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb`` and ``wbu``. For instance, to open \n a :term:`BAM` formatted file for reading, type::\n\n f = pysam.Samfile('ex1.bam','rb')\n\n If mode is not specified, we will try to auto-detect in the order 'rb', 'r', thus both the following\n should work::\n\n f1 = pysam.Samfile('ex1.bam' )\n f2 = pysam.Samfile('ex1.sam' )\n\n If an index for a BAM file exists (.bai), it will be opened automatically. Without an index random\n access to reads via :meth:`fetch` and :meth:`pileup` is disabled.\n\n For writing, the header of a :term:`SAM` file/:term:`BAM` file can be constituted from several\n sources (see also the samtools format specification):\n\n 1. If *template* is given, the header is copied from a another *Samfile* \n (*template* must be of type *Samfile*).\n\n 2. If *header* is given, the header is built from a multi-level dictionary. The first level \n are the four types ('HD', 'SQ', ...). The second level are a list of lines, with each line \n being a list of tag-value pairs.\n\n 3. If *text* is given, new header text is copied from raw text.\n\n 4. The names (*referencenames*) and lengths (*referencelengths*) are supplied directly as lists. \n By default, 'SQ' and 'LN' tags will be added to the header text. This option can be\n changed by unsetting the flag *add_sq_text*. \n\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_18IteratorRowAllRefs___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_18IteratorRowAllRefs___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/
+ __pyx_pf_9csamtools_7Samfile_20__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_7Samfile_21__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_Samfile, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_9csamtools_Samfile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowAllRefs, /*tp_new*/
+ __pyx_tp_new_9csamtools_Samfile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection __pyx_vtable_9csamtools_IteratorRowSelection;
-static PyObject *__pyx_tp_new_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowSelection *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRow(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorRowSelection *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowSelection;
- p->positions = Py_None; Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_20IteratorRowSelection___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorRowSelection(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_9csamtools_20IteratorRowSelection___dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- Py_XDECREF(p->positions);
- __pyx_tp_dealloc_9csamtools_IteratorRow(o);
-}
-
-static int __pyx_tp_traverse_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
- e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
- }
- if (p->positions) {
- e = (*v)(p->positions, a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_9csamtools_IteratorRowSelection(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
- PyObject* tmp;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
- __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
- }
- tmp = ((PyObject*)p->positions);
- p->positions = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
+static void __pyx_tp_dealloc_9csamtools_IteratorRow(PyObject *o) {
+ (*Py_TYPE(o)->tp_free)(o);
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowSelection[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorRowSelection___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection___next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorRow[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorRowSelection = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRow = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowSelection = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRow = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRowSelection = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRow = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRow = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRow = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowSelection"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowSelection), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRow"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRow), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowSelection, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRow, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRowSelection, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowSelection, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowSelection, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRow, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRow, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRow, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowSelection, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorRowSelection, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorRowSelection, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorRow, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("abstract base class for iterators over mapped reads.\n\n Various iterators implement different behaviours for wrapping around\n contig boundaries. Examples include:\n\n :class:`pysam.IteratorRowRegion`\n iterate within a single contig and a defined region.\n\n :class:`pysam.IteratorRowAll`\n iterate until EOF. This iterator will also include unmapped reads.\n\n :class:`pysam.IteratorRowAllRefs`\n iterate over all reads in all reference sequences.\n \n The method :meth:`Samfile.fetch` returns an IteratorRow.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_20IteratorRowSelection___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_20IteratorRowSelection___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowSelection, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRow, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowSelection, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRow, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_vtable_9csamtools_IteratorColumn;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowAll __pyx_vtable_9csamtools_IteratorRowAll;
-static PyObject *__pyx_tp_new_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorColumn *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowAll *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorColumn *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorColumn;
- p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
- p->stepper = Py_None; Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_14IteratorColumn___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowAll *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowAll;
+ if (__pyx_pf_9csamtools_14IteratorRowAll___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorColumn(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
+static void __pyx_tp_dealloc_9csamtools_IteratorRowAll(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_14IteratorColumn___dealloc__(o);
+ __pyx_pf_9csamtools_14IteratorRowAll_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_XDECREF(((PyObject *)p->iter));
- Py_XDECREF(((PyObject *)p->samfile));
- Py_XDECREF(((PyObject *)p->fastafile));
- Py_XDECREF(p->stepper);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
- if (p->iter) {
- e = (*v)(((PyObject*)p->iter), a); if (e) return e;
- }
- if (p->samfile) {
- e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
- }
- if (p->fastafile) {
- e = (*v)(((PyObject*)p->fastafile), a); if (e) return e;
- }
- if (p->stepper) {
- e = (*v)(p->stepper, a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_9csamtools_IteratorColumn(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->iter);
- p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->fastafile);
- p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->stepper);
- p->stepper = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyObject *__pyx_getprop_9csamtools_14IteratorColumn_seq_len(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(o);
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = {
- {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_addReference)},
- {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_hasReference)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowAll[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_14IteratorRowAll_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll_2__next__)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_IteratorColumn[] = {
- {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_161), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_IteratorColumn = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowAll = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorColumn = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAll = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorColumn = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAll = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorColumn"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorColumn), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowAll"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowAll), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowAll, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorColumn, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorColumn, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorColumn, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRowAll, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowAll, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowAll, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorColumn, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("abstract base class for iterators over columns.\n\n IteratorColumn objects wrap the pileup functionality of samtools.\n \n For reasons of efficiency, the iterator points to the current \n pileup buffer. The pileup buffer is updated at every iteration.\n This might cause some unexpected behavious. For example,\n consider the conversion to a list::\n \n f = Samfile(\"file.bam\", \"rb\")\n result = list( f.pileup() )\n\n Here, ``result`` will contain ``n`` objects of type :class:`PileupProxy` for ``n`` columns, \n but each object in ``result`` will contain the same information.\n \n The desired behaviour can be achieved by list comprehension::\n\n result = [ x.pileups() for x in f.pileup() ]\n\n ``result`` will be a list of ``n`` lists of objects of type :class:`PileupRead`.\n\n If the iterator is associated with a :class:`Fastafile` using the :meth:`addReference`\n method, then the iterator will export the current sequence via the methods :meth:`getSequence`\n and :meth:`seq_len`.\n\n Optional kwargs to the iterator\n\n stepper\n The stepper controlls how the iterator advances. \n Possible options for the stepper are \n \n all\n use all reads for pileup.\n samtools\n same filter and read processing as in :term:`csamtools` pileup\n fastafile\n A :class:`FastaFile` object\n mask\n Skip all reads with bits set in mask.\n \n \n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorRowAll, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("*(Samfile samfile, int reopen = True)*\n\n iterate over all reads in *samfile*\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_14IteratorColumn___iter__, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/
+ __pyx_pf_9csamtools_14IteratorRowAll_1__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_14IteratorRowAll_2__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_IteratorColumn, /*tp_getset*/
+ 0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorColumn, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowAll, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion __pyx_vtable_9csamtools_IteratorColumnRegion;
-static PyObject *__pyx_tp_new_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorColumnRegion *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_PileupProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnRegion;
- if (__pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorColumnRegion___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion___next__)},
+static void __pyx_tp_dealloc_9csamtools_PileupProxy(PyObject *o) {
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_tid(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11PileupProxy_3tid___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_n(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11PileupProxy_1n___get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pos(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11PileupProxy_3pos___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pileups(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11PileupProxy_7pileups___get__(o);
+}
+
+static PyMethodDef __pyx_methods_9csamtools_PileupProxy[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorColumnRegion = {
+static struct PyGetSetDef __pyx_getsets_9csamtools_PileupProxy[] = {
+ {(char *)"tid", __pyx_getprop_9csamtools_11PileupProxy_tid, 0, __Pyx_DOCSTR(__pyx_k_214), 0},
+ {(char *)"n", __pyx_getprop_9csamtools_11PileupProxy_n, __pyx_setprop_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_215), 0},
+ {(char *)"pos", __pyx_getprop_9csamtools_11PileupProxy_pos, 0, 0, 0},
+ {(char *)"pileups", __pyx_getprop_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_216), 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_PileupProxy = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnRegion = {
+static PySequenceMethods __pyx_tp_as_sequence_PileupProxy = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnRegion = {
+static PyMappingMethods __pyx_tp_as_mapping_PileupProxy = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = {
+static PyBufferProcs __pyx_tp_as_buffer_PileupProxy = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
+static PyTypeObject __pyx_type_9csamtools_PileupProxy = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorColumnRegion"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorColumnRegion), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.PileupProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_PileupProxy), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_PileupProxy, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorColumnRegion, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorColumnRegion, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorColumnRegion, /*tp_as_mapping*/
+ &__pyx_tp_as_number_PileupProxy, /*tp_as_number*/
+ &__pyx_tp_as_sequence_PileupProxy, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_PileupProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- 0, /*tp_str*/
+ __pyx_pf_9csamtools_11PileupProxy_1__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorColumnRegion, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("iterates over a region only.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
+ &__pyx_tp_as_buffer_PileupProxy, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("PileupProxy()\nA pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column \n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n\n This class is a proxy for results returned by the samtools pileup engine.\n If the underlying engine iterator advances, the results of this column\n will change.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
- __pyx_pf_9csamtools_20IteratorColumnRegion___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorColumnRegion, /*tp_methods*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_PileupProxy, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_9csamtools_PileupProxy, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- 0, /*tp_init*/
+ __pyx_pf_9csamtools_11PileupProxy___init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorColumnRegion, /*tp_new*/
+ __pyx_tp_new_9csamtools_PileupProxy, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs __pyx_vtable_9csamtools_IteratorColumnAllRefs;
-static PyObject *__pyx_tp_new_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorColumnAllRefs *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
- if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
- if (__pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
- return o;
+static PyObject *__pyx_tp_new_9csamtools_PileupRead(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_PileupRead *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_9csamtools_PileupRead *)o);
+ p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
+ return o;
+}
+
+static void __pyx_tp_dealloc_9csamtools_PileupRead(PyObject *o) {
+ struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
+ Py_XDECREF(((PyObject *)p->_alignment));
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_9csamtools_PileupRead(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
+ if (p->_alignment) {
+ e = (*v)(((PyObject*)p->_alignment), a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_9csamtools_PileupRead(PyObject *o) {
+ struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->_alignment);
+ p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_alignment(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_9alignment___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_qpos(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_4qpos___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_indel(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_5indel___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_del(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_6is_del___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_head(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_7is_head___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_tail(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_7is_tail___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_level(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_5level___get__(o);
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorColumnAllRefs[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_21IteratorColumnAllRefs___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs___next__)},
+static PyMethodDef __pyx_methods_9csamtools_PileupRead[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = {
+static struct PyGetSetDef __pyx_getsets_9csamtools_PileupRead[] = {
+ {(char *)"alignment", __pyx_getprop_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_217), 0},
+ {(char *)"qpos", __pyx_getprop_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_218), 0},
+ {(char *)"indel", __pyx_getprop_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_219), 0},
+ {(char *)"is_del", __pyx_getprop_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_220), 0},
+ {(char *)"is_head", __pyx_getprop_9csamtools_10PileupRead_is_head, 0, 0, 0},
+ {(char *)"is_tail", __pyx_getprop_9csamtools_10PileupRead_is_tail, 0, 0, 0},
+ {(char *)"level", __pyx_getprop_9csamtools_10PileupRead_level, 0, 0, 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_PileupRead = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnAllRefs = {
+static PySequenceMethods __pyx_tp_as_sequence_PileupRead = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnAllRefs = {
+static PyMappingMethods __pyx_tp_as_mapping_PileupRead = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = {
+static PyBufferProcs __pyx_tp_as_buffer_PileupRead = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = {
+static PyTypeObject __pyx_type_9csamtools_PileupRead = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorColumnAllRefs"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.PileupRead"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_PileupRead), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_PileupRead, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorColumnAllRefs, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorColumnAllRefs, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorColumnAllRefs, /*tp_as_mapping*/
+ &__pyx_tp_as_number_PileupRead, /*tp_as_number*/
+ &__pyx_tp_as_sequence_PileupRead, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_PileupRead, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- 0, /*tp_str*/
+ __pyx_pf_9csamtools_10PileupRead_1__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorColumnAllRefs, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("iterates over all columns by chaining iterators over each reference\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
+ &__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("PileupRead()\nA read aligned to a column.\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_PileupRead, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_PileupRead, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
- __pyx_pf_9csamtools_21IteratorColumnAllRefs___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorColumnAllRefs, /*tp_methods*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_PileupRead, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_9csamtools_PileupRead, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- 0, /*tp_init*/
+ __pyx_pf_9csamtools_10PileupRead___init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorColumnAllRefs, /*tp_new*/
+ __pyx_tp_new_9csamtools_PileupRead, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_9csamtools_Fastafile __pyx_vtable_9csamtools_Fastafile;
-static PyObject *__pyx_tp_new_9csamtools_SNPCall(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_9csamtools_Fastafile(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_Fastafile *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
+ p = ((struct __pyx_obj_9csamtools_Fastafile *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_Fastafile;
+ if (__pyx_pf_9csamtools_9Fastafile___cinit__(o, a, k) < 0) {
+ Py_DECREF(o); o = 0;
+ }
return o;
}
-static void __pyx_tp_dealloc_9csamtools_SNPCall(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) {
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pf_9csamtools_9Fastafile_5__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_tid(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_3tid___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_pos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_3pos___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_reference_base(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_14reference_base___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_genotype(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_8genotype___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_consensus_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_snp_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_mapping_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_coverage(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_8coverage___get__(o);
+static PyObject *__pyx_getprop_9csamtools_9Fastafile_filename(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_9Fastafile_8filename___get__(o);
}
-static PyMethodDef __pyx_methods_9csamtools_SNPCall[] = {
+static PyMethodDef __pyx_methods_9csamtools_Fastafile[] = {
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_1_isOpen)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_3_open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_3_open)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_4close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_4close)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_6fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_6fetch)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_SNPCall[] = {
- {(char *)"tid", __pyx_getprop_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_154), 0},
- {(char *)"pos", __pyx_getprop_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_162), 0},
- {(char *)"reference_base", __pyx_getprop_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_163), 0},
- {(char *)"genotype", __pyx_getprop_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_164), 0},
- {(char *)"consensus_quality", __pyx_getprop_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_165), 0},
- {(char *)"snp_quality", __pyx_getprop_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_166), 0},
- {(char *)"mapping_quality", __pyx_getprop_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_167), 0},
- {(char *)"coverage", __pyx_getprop_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_168), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_Fastafile[] = {
+ {(char *)"filename", __pyx_getprop_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_206), 0},
{0, 0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_SNPCall = {
+static PyNumberMethods __pyx_tp_as_number_Fastafile = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_SNPCall = {
- 0, /*sq_length*/
+static PySequenceMethods __pyx_tp_as_sequence_Fastafile = {
+ __pyx_pf_9csamtools_9Fastafile_2__len__, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_item*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_SNPCall = {
- 0, /*mp_length*/
+static PyMappingMethods __pyx_tp_as_mapping_Fastafile = {
+ __pyx_pf_9csamtools_9Fastafile_2__len__, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_SNPCall = {
+static PyBufferProcs __pyx_tp_as_buffer_Fastafile = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_SNPCall = {
+static PyTypeObject __pyx_type_9csamtools_Fastafile = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.SNPCall"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_SNPCall), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.Fastafile"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_Fastafile), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_SNPCall, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_Fastafile, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_SNPCall, /*tp_as_number*/
- &__pyx_tp_as_sequence_SNPCall, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_SNPCall, /*tp_as_mapping*/
+ &__pyx_tp_as_number_Fastafile, /*tp_as_number*/
+ &__pyx_tp_as_sequence_Fastafile, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_Fastafile, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pf_9csamtools_7SNPCall___str__, /*tp_str*/
+ 0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_SNPCall, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("the results of a SNP call."), /*tp_doc*/
+ &__pyx_tp_as_buffer_Fastafile, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("*(filename)*\n \n A *FASTA* file. The file is automatically opened.\n\n The file expects an indexed fasta file.\n\n TODO: \n add automatic indexing.\n add function to get sequence names.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_9csamtools_SNPCall, /*tp_methods*/
+ __pyx_methods_9csamtools_Fastafile, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_SNPCall, /*tp_getset*/
+ __pyx_getsets_9csamtools_Fastafile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_SNPCall, /*tp_new*/
+ __pyx_tp_new_9csamtools_Fastafile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_SNPCallerBase __pyx_vtable_9csamtools_SNPCallerBase;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion __pyx_vtable_9csamtools_IteratorRowRegion;
-static PyObject *__pyx_tp_new_9csamtools_SNPCallerBase(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_SNPCallerBase *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_SNPCallerBase *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_SNPCallerBase;
- p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_13SNPCallerBase___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowRegion;
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pf_9csamtools_17IteratorRowRegion___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_SNPCallerBase(PyObject *o) {
- struct __pyx_obj_9csamtools_SNPCallerBase *p = (struct __pyx_obj_9csamtools_SNPCallerBase *)o;
+static void __pyx_tp_dealloc_9csamtools_IteratorRowRegion(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_13SNPCallerBase___dealloc__(o);
+ __pyx_pf_9csamtools_17IteratorRowRegion_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_XDECREF(((PyObject *)p->iter));
- (*Py_TYPE(o)->tp_free)(o);
+ Py_XDECREF(((PyObject *)p->samfile));
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static int __pyx_tp_traverse_9csamtools_SNPCallerBase(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_9csamtools_SNPCallerBase *p = (struct __pyx_obj_9csamtools_SNPCallerBase *)o;
- if (p->iter) {
- e = (*v)(((PyObject*)p->iter), a); if (e) return e;
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
+ e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ }
+ if (p->samfile) {
+ e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_9csamtools_SNPCallerBase(PyObject *o) {
- struct __pyx_obj_9csamtools_SNPCallerBase *p = (struct __pyx_obj_9csamtools_SNPCallerBase *)o;
+static int __pyx_tp_clear_9csamtools_IteratorRowRegion(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
PyObject* tmp;
- tmp = ((PyObject*)p->iter);
- p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
+ __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+ }
+ tmp = ((PyObject*)p->samfile);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_9csamtools_SNPCallerBase[] = {
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowRegion[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_17IteratorRowRegion_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion_2__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_SNPCallerBase = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowRegion = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_SNPCallerBase = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowRegion = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_SNPCallerBase = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowRegion = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_SNPCallerBase = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_SNPCallerBase = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.SNPCallerBase"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_SNPCallerBase), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowRegion"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowRegion), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_SNPCallerBase, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowRegion, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_SNPCallerBase, /*tp_as_number*/
- &__pyx_tp_as_sequence_SNPCallerBase, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_SNPCallerBase, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRowRegion, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowRegion, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowRegion, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_SNPCallerBase, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("Base class for SNP callers.\n\n *min_baseQ*\n minimum base quality (possibly capped by BAQ)\n *capQ_threshold*\n coefficient for adjusting mapQ of poor mappings\n *theta*\n theta in maq consensus calling model\n *n_haplotypes*\n number of haplotypes in the sample\n *het_rate*\n prior of a difference between two haplotypes\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_SNPCallerBase, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_SNPCallerBase, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorRowRegion, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("*(Samfile samfile, int tid, int beg, int end, int reopen = True )*\n\n iterate over mapped reads in a region.\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n The samtools iterators assume that the file\n position between iterations do not change.\n As a consequence, no two iterators can work\n on the same file. To permit this, each iterator\n creates its own file handle by re-opening the\n file.\n\n Note that the index will be shared between \n samfile and the iterator.\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_IteratorRowRegion, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowRegion, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_SNPCallerBase, /*tp_methods*/
+ __pyx_pf_9csamtools_17IteratorRowRegion_1__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_17IteratorRowRegion_2__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowRegion, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_SNPCallerBase, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowRegion, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorSNPCalls __pyx_vtable_9csamtools_IteratorSNPCalls;
-static PyObject *__pyx_tp_new_9csamtools_IteratorSNPCalls(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorSNPCalls *p;
- PyObject *o = __pyx_tp_new_9csamtools_SNPCallerBase(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorSNPCalls *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_SNPCallerBase*)__pyx_vtabptr_9csamtools_IteratorSNPCalls;
- if (__pyx_pf_9csamtools_16IteratorSNPCalls___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorSNPCalls[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_16IteratorSNPCalls___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_16IteratorSNPCalls___next__)},
+static void __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ Py_XDECREF(((PyObject *)p->samfile));
+ Py_XDECREF(((PyObject *)p->rowiter));
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+}
+
+static int __pyx_tp_traverse_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
+ e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ }
+ if (p->samfile) {
+ e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
+ }
+ if (p->rowiter) {
+ e = (*v)(((PyObject*)p->rowiter), a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ PyObject* tmp;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
+ __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+ }
+ tmp = ((PyObject*)p->samfile);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->rowiter);
+ p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = {
+ {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_1nextiter)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorSNPCalls = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorSNPCalls = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorSNPCalls = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAllRefs = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorSNPCalls = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorSNPCalls = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorSNPCalls"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorSNPCalls), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_SNPCallerBase, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorSNPCalls, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorSNPCalls, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorSNPCalls, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRowAllRefs, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowAllRefs, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowAllRefs, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorSNPCalls, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("*(IteratorColumn iterator)*\n\n call SNPs within a region.\n\n *iterator* is a pileup iterator. SNPs will be called\n on all positions returned by this iterator.\n\n This caller is fast if SNPs are called over large continuous\n regions. It is slow, if instantiated frequently and in random\n order as the sequence will have to be reloaded.\n\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_SNPCallerBase, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_SNPCallerBase, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_16IteratorSNPCalls___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_16IteratorSNPCalls___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorSNPCalls, /*tp_methods*/
+ __pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorSNPCalls, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowAllRefs, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_SNPCaller __pyx_vtable_9csamtools_SNPCaller;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection __pyx_vtable_9csamtools_IteratorRowSelection;
-static PyObject *__pyx_tp_new_9csamtools_SNPCaller(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_SNPCaller *p;
- PyObject *o = __pyx_tp_new_9csamtools_SNPCallerBase(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_SNPCaller *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_SNPCallerBase*)__pyx_vtabptr_9csamtools_SNPCaller;
- if (__pyx_pf_9csamtools_9SNPCaller___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowSelection *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowSelection;
+ p->positions = Py_None; Py_INCREF(Py_None);
+ if (__pyx_pf_9csamtools_20IteratorRowSelection___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_SNPCaller[] = {
- {__Pyx_NAMESTR("call"), (PyCFunction)__pyx_pf_9csamtools_9SNPCaller_call, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9SNPCaller_call)},
+static void __pyx_tp_dealloc_9csamtools_IteratorRowSelection(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ Py_XDECREF(p->positions);
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+}
+
+static int __pyx_tp_traverse_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
+ e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ }
+ if (p->positions) {
+ e = (*v)(p->positions, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_9csamtools_IteratorRowSelection(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
+ PyObject* tmp;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
+ __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+ }
+ tmp = ((PyObject*)p->positions);
+ p->positions = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowSelection[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorRowSelection_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection_2__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_SNPCaller = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowSelection = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_SNPCaller = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowSelection = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_SNPCaller = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowSelection = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_SNPCaller = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_SNPCaller = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.SNPCaller"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_SNPCaller), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowSelection"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowSelection), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_SNPCallerBase, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowSelection, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_SNPCaller, /*tp_as_number*/
- &__pyx_tp_as_sequence_SNPCaller, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_SNPCaller, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRowSelection, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowSelection, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowSelection, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_SNPCaller, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("*(IteratorColumn iterator_column )*\n\n The samtools SNP caller.\n\n This object will call SNPs in *samfile* against the reference\n sequence in *fasta*.\n\n This caller is fast for calling few SNPs in selected regions.\n\n It is slow, if called over large genomic regions.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_SNPCallerBase, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_SNPCallerBase, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorRowSelection, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_IteratorRowSelection, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowSelection, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_SNPCaller, /*tp_methods*/
+ __pyx_pf_9csamtools_20IteratorRowSelection_1__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_20IteratorRowSelection_2__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowSelection, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_SNPCaller, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowSelection, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_vtable_9csamtools_IteratorColumn;
-static PyObject *__pyx_tp_new_9csamtools_IndelCall(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorColumn *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- if (__pyx_pf_9csamtools_9IndelCall___cinit__(o, __pyx_empty_tuple, NULL) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorColumn *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorColumn;
+ p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
+ p->stepper = Py_None; Py_INCREF(Py_None);
+ if (__pyx_pf_9csamtools_14IteratorColumn___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IndelCall(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_IteratorColumn(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_9IndelCall___dealloc__(o);
+ __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
+ Py_XDECREF(((PyObject *)p->iter));
+ Py_XDECREF(((PyObject *)p->samfile));
+ Py_XDECREF(((PyObject *)p->fastafile));
+ Py_XDECREF(p->stepper);
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_tid(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_3tid___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_pos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_3pos___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_genotype(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_8genotype___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_consensus_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_17consensus_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_snp_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_11snp_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_mapping_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_15mapping_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_coverage(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_8coverage___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_first_allele(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_12first_allele___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_second_allele(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_13second_allele___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_reads_first(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_11reads_first___get__(o);
+static int __pyx_tp_traverse_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
+ if (p->iter) {
+ e = (*v)(((PyObject*)p->iter), a); if (e) return e;
+ }
+ if (p->samfile) {
+ e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
+ }
+ if (p->fastafile) {
+ e = (*v)(((PyObject*)p->fastafile), a); if (e) return e;
+ }
+ if (p->stepper) {
+ e = (*v)(p->stepper, a); if (e) return e;
+ }
+ return 0;
}
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_reads_second(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_12reads_second___get__(o);
+static int __pyx_tp_clear_9csamtools_IteratorColumn(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->iter);
+ p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->samfile);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->fastafile);
+ p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->stepper);
+ p->stepper = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
}
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_reads_diff(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_10reads_diff___get__(o);
+static PyObject *__pyx_getprop_9csamtools_14IteratorColumn_seq_len(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(o);
}
-static PyMethodDef __pyx_methods_9csamtools_IndelCall[] = {
+static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = {
+ {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_2addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_2addReference)},
+ {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_3hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_3hasReference)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_IndelCall[] = {
- {(char *)"tid", __pyx_getprop_9csamtools_9IndelCall_tid, 0, __Pyx_DOCSTR(__pyx_k_154), 0},
- {(char *)"pos", __pyx_getprop_9csamtools_9IndelCall_pos, 0, __Pyx_DOCSTR(__pyx_k_162), 0},
- {(char *)"genotype", __pyx_getprop_9csamtools_9IndelCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_164), 0},
- {(char *)"consensus_quality", __pyx_getprop_9csamtools_9IndelCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_165), 0},
- {(char *)"snp_quality", __pyx_getprop_9csamtools_9IndelCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_166), 0},
- {(char *)"mapping_quality", __pyx_getprop_9csamtools_9IndelCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_167), 0},
- {(char *)"coverage", __pyx_getprop_9csamtools_9IndelCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_168), 0},
- {(char *)"first_allele", __pyx_getprop_9csamtools_9IndelCall_first_allele, 0, __Pyx_DOCSTR(__pyx_k_169), 0},
- {(char *)"second_allele", __pyx_getprop_9csamtools_9IndelCall_second_allele, 0, __Pyx_DOCSTR(__pyx_k_170), 0},
- {(char *)"reads_first", __pyx_getprop_9csamtools_9IndelCall_reads_first, 0, __Pyx_DOCSTR(__pyx_k_171), 0},
- {(char *)"reads_second", __pyx_getprop_9csamtools_9IndelCall_reads_second, 0, __Pyx_DOCSTR(__pyx_k_171), 0},
- {(char *)"reads_diff", __pyx_getprop_9csamtools_9IndelCall_reads_diff, 0, __Pyx_DOCSTR(__pyx_k_171), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_IteratorColumn[] = {
+ {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_221), 0},
{0, 0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IndelCall = {
+static PyNumberMethods __pyx_tp_as_number_IteratorColumn = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IndelCall = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorColumn = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IndelCall = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorColumn = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IndelCall = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IndelCall = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IndelCall"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IndelCall), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumn"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumn), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IndelCall, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IndelCall, /*tp_as_number*/
- &__pyx_tp_as_sequence_IndelCall, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IndelCall, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorColumn, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorColumn, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorColumn, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pf_9csamtools_9IndelCall___str__, /*tp_str*/
+ 0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IndelCall, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("the results of an indel call."), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorColumn, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("abstract base class for iterators over columns.\n\n IteratorColumn objects wrap the pileup functionality of samtools.\n \n For reasons of efficiency, the iterator points to the current \n pileup buffer. The pileup buffer is updated at every iteration.\n This might cause some unexpected behavious. For example,\n consider the conversion to a list::\n \n f = Samfile(\"file.bam\", \"rb\")\n result = list( f.pileup() )\n\n Here, ``result`` will contain ``n`` objects of type :class:`PileupProxy` for ``n`` columns, \n but each object in ``result`` will contain the same information.\n \n The desired behaviour can be achieved by list comprehension::\n\n result = [ x.pileups() for x in f.pileup() ]\n\n ``result`` will be a list of ``n`` lists of objects of type :class:`PileupRead`.\n\n If the iterator is associated with a :class:`Fastafile` using the :meth:`addReference`\n method, then the iterator will export the current sequence via the methods :meth:`getSequence`\n and :meth:`seq_len`.\n\n Optional kwargs to the iterator\n\n stepper\n The stepper controlls how the iterator advances. \n Possible options for the stepper are \n \n all\n use all reads for pileup.\n samtools\n same filter and read processing as in :term:`csamtools` pileup\n fastafile\n A :class:`FastaFile` object\n mask\n Skip all reads with bits set in mask.\n max_depth\n maximum read depth. The default is 8000.\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
+ __pyx_pf_9csamtools_14IteratorColumn_1__iter__, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_9csamtools_IndelCall, /*tp_methods*/
+ __pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_IndelCall, /*tp_getset*/
+ __pyx_getsets_9csamtools_IteratorColumn, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IndelCall, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorColumn, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion __pyx_vtable_9csamtools_IteratorColumnRegion;
-static PyObject *__pyx_tp_new_9csamtools_IndelCallerBase(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IndelCallerBase *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
+static PyObject *__pyx_tp_new_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorColumnRegion *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IndelCallerBase *)o);
- p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_15IndelCallerBase___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnRegion;
+ if (__pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IndelCallerBase(PyObject *o) {
- struct __pyx_obj_9csamtools_IndelCallerBase *p = (struct __pyx_obj_9csamtools_IndelCallerBase *)o;
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_9csamtools_15IndelCallerBase___dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- Py_XDECREF(((PyObject *)p->iter));
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_9csamtools_IndelCallerBase(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_9csamtools_IndelCallerBase *p = (struct __pyx_obj_9csamtools_IndelCallerBase *)o;
- if (p->iter) {
- e = (*v)(((PyObject*)p->iter), a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_9csamtools_IndelCallerBase(PyObject *o) {
- struct __pyx_obj_9csamtools_IndelCallerBase *p = (struct __pyx_obj_9csamtools_IndelCallerBase *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->iter);
- p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyMethodDef __pyx_methods_9csamtools_IndelCallerBase[] = {
- {__Pyx_NAMESTR("_call"), (PyCFunction)__pyx_pf_9csamtools_15IndelCallerBase__call, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_15IndelCallerBase__call)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion_1__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IndelCallerBase = {
+static PyNumberMethods __pyx_tp_as_number_IteratorColumnRegion = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IndelCallerBase = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnRegion = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IndelCallerBase = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnRegion = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IndelCallerBase = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IndelCallerBase = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IndelCallerBase"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IndelCallerBase), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumnRegion"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumnRegion), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IndelCallerBase, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IndelCallerBase, /*tp_as_number*/
- &__pyx_tp_as_sequence_IndelCallerBase, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IndelCallerBase, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorColumnRegion, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorColumnRegion, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorColumnRegion, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IndelCallerBase, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("Base class for SNP callers.\n\n *min_baseQ*\n minimum base quality (possibly capped by BAQ)\n *capQ_threshold*\n coefficient for adjusting mapQ of poor mappings\n *theta*\n theta in maq consensus calling model\n *n_haplotypes*\n number of haplotypes in the sample\n *het_rate*\n prior of a difference between two haplotypes\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IndelCallerBase, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IndelCallerBase, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorColumnRegion, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("iterates over a region only.\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_IndelCallerBase, /*tp_methods*/
+ __pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorColumnRegion, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IndelCallerBase, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorColumnRegion, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs __pyx_vtable_9csamtools_IteratorColumnAllRefs;
-static PyObject *__pyx_tp_new_9csamtools_IndelCaller(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = __pyx_tp_new_9csamtools_IndelCallerBase(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorColumnAllRefs *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
if (!o) return 0;
- if (__pyx_pf_9csamtools_11IndelCaller___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
+ if (__pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IndelCaller[] = {
- {__Pyx_NAMESTR("call"), (PyCFunction)__pyx_pf_9csamtools_11IndelCaller_call, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11IndelCaller_call)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorColumnAllRefs[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IndelCaller = {
+static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IndelCaller = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnAllRefs = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IndelCaller = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnAllRefs = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IndelCaller = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IndelCaller = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IndelCaller"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IndelCaller), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumnAllRefs"), /*tp_name*/
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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- if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- if (__Pyx_SetVtable(__pyx_type_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __pyx_vtable_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_cnext;
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- {
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- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowAllRefs = &__pyx_type_9csamtools_IteratorRowAllRefs;
- __pyx_vtabptr_9csamtools_IteratorRowSelection = &__pyx_vtable_9csamtools_IteratorRowSelection;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent;
- __pyx_vtable_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_cnext;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (void(*)(void))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowSelection.cnext = (void(*)(void))__pyx_f_9csamtools_20IteratorRowSelection_cnext;
- #endif
- __pyx_type_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowSelection = &__pyx_type_9csamtools_IteratorRowSelection;
- __pyx_vtabptr_9csamtools_IteratorColumn = &__pyx_vtable_9csamtools_IteratorColumn;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_cnext;
- __pyx_vtable_9csamtools_IteratorColumn.getSequence = (char *(*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_getSequence;
- __pyx_vtable_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_setMask;
- __pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData;
- __pyx_vtable_9csamtools_IteratorColumn.reset = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_reset;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.cnext = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_cnext;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.getSequence = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_getSequence;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.setMask = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_setMask;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.reset = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_reset;
- #endif
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorColumn = &__pyx_type_9csamtools_IteratorColumn;
- __pyx_vtabptr_9csamtools_IteratorColumnRegion = &__pyx_vtable_9csamtools_IteratorColumnRegion;
- __pyx_vtable_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
- __pyx_type_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorColumnRegion = &__pyx_type_9csamtools_IteratorColumnRegion;
- __pyx_vtabptr_9csamtools_IteratorColumnAllRefs = &__pyx_vtable_9csamtools_IteratorColumnAllRefs;
- __pyx_vtable_9csamtools_IteratorColumnAllRefs.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
- __pyx_type_9csamtools_IteratorColumnAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs___next__.doc = __pyx_doc_9csamtools_21IteratorColumnAllRefs___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorColumnAllRefs = &__pyx_type_9csamtools_IteratorColumnAllRefs;
- if (PyType_Ready(&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_SNPCall = &__pyx_type_9csamtools_SNPCall;
- __pyx_vtabptr_9csamtools_SNPCallerBase = &__pyx_vtable_9csamtools_SNPCallerBase;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_SNPCallerBase.__dump = (PyObject *(*)(struct __pyx_obj_9csamtools_SNPCallerBase *, glf1_t *, uint32_t, int))__pyx_f_9csamtools_13SNPCallerBase___dump;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_SNPCallerBase.__dump = (void(*)(void))__pyx_f_9csamtools_13SNPCallerBase___dump;
- #endif
- if (PyType_Ready(&__pyx_type_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_SNPCallerBase.tp_dict, __pyx_vtabptr_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "SNPCallerBase", (PyObject *)&__pyx_type_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_SNPCallerBase = &__pyx_type_9csamtools_SNPCallerBase;
- __pyx_vtabptr_9csamtools_IteratorSNPCalls = &__pyx_vtable_9csamtools_IteratorSNPCalls;
- __pyx_vtable_9csamtools_IteratorSNPCalls.__pyx_base = *__pyx_vtabptr_9csamtools_SNPCallerBase;
- __pyx_type_9csamtools_IteratorSNPCalls.tp_base = __pyx_ptype_9csamtools_SNPCallerBase;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorSNPCalls, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_16IteratorSNPCalls___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_16IteratorSNPCalls___next__.doc = __pyx_doc_9csamtools_16IteratorSNPCalls___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_16IteratorSNPCalls___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorSNPCalls.tp_dict, __pyx_vtabptr_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorSNPCalls", (PyObject *)&__pyx_type_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorSNPCalls = &__pyx_type_9csamtools_IteratorSNPCalls;
- __pyx_vtabptr_9csamtools_SNPCaller = &__pyx_vtable_9csamtools_SNPCaller;
- __pyx_vtable_9csamtools_SNPCaller.__pyx_base = *__pyx_vtabptr_9csamtools_SNPCallerBase;
- __pyx_type_9csamtools_SNPCaller.tp_base = __pyx_ptype_9csamtools_SNPCallerBase;
- if (PyType_Ready(&__pyx_type_9csamtools_SNPCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_SNPCaller.tp_dict, __pyx_vtabptr_9csamtools_SNPCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "SNPCaller", (PyObject *)&__pyx_type_9csamtools_SNPCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_SNPCaller = &__pyx_type_9csamtools_SNPCaller;
- if (PyType_Ready(&__pyx_type_9csamtools_IndelCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndelCall", (PyObject *)&__pyx_type_9csamtools_IndelCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IndelCall = &__pyx_type_9csamtools_IndelCall;
- if (PyType_Ready(&__pyx_type_9csamtools_IndelCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndelCallerBase", (PyObject *)&__pyx_type_9csamtools_IndelCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IndelCallerBase = &__pyx_type_9csamtools_IndelCallerBase;
- __pyx_type_9csamtools_IndelCaller.tp_base = __pyx_ptype_9csamtools_IndelCallerBase;
- if (PyType_Ready(&__pyx_type_9csamtools_IndelCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndelCaller", (PyObject *)&__pyx_type_9csamtools_IndelCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IndelCaller = &__pyx_type_9csamtools_IndelCaller;
- __pyx_type_9csamtools_IteratorIndelCalls.tp_base = __pyx_ptype_9csamtools_IndelCallerBase;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorIndelCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorIndelCalls, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_18IteratorIndelCalls___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_18IteratorIndelCalls___next__.doc = __pyx_doc_9csamtools_18IteratorIndelCalls___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorIndelCalls___next__;
- }
- }
- if (__Pyx_SetAttrString(__pyx_m, "IteratorIndelCalls", (PyObject *)&__pyx_type_9csamtools_IteratorIndelCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorIndelCalls = &__pyx_type_9csamtools_IteratorIndelCalls;
- if (PyType_Ready(&__pyx_type_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndexedReads", (PyObject *)&__pyx_type_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IndexedReads = &__pyx_type_9csamtools_IndexedReads;
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- __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /*--- Function import code ---*/
- /*--- Execution code ---*/
+ __pyx_builtin_IOError = __Pyx_GetName(__pyx_b, __pyx_n_s__IOError); if (!__pyx_builtin_IOError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_OverflowError = __Pyx_GetName(__pyx_b, __pyx_n_s__OverflowError); if (!__pyx_builtin_OverflowError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_NotImplementedError = __Pyx_GetName(__pyx_b, __pyx_n_s__NotImplementedError); if (!__pyx_builtin_NotImplementedError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_OSError = __Pyx_GetName(__pyx_b, __pyx_n_s__OSError); if (!__pyx_builtin_OSError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_AttributeError = __Pyx_GetName(__pyx_b, __pyx_n_s__AttributeError); if (!__pyx_builtin_AttributeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, __pyx_n_s__StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_cmp = __Pyx_GetName(__pyx_b, __pyx_n_s__cmp); if (!__pyx_builtin_cmp) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2018; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_chr = __Pyx_GetName(__pyx_b, __pyx_n_s__chr); if (!__pyx_builtin_chr) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2633; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_TypeError = __Pyx_GetName(__pyx_b, __pyx_n_s__TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ return 0;
+ __pyx_L1_error:;
+ return -1;
+}
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- * # cython: profile=True
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- * import os
- * import sys
+static int __Pyx_InitCachedConstants(void) {
+ __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants");
+
+ /* "csamtools.pyx":271
+ * def __len__(self):
+ * if self.fastafile == NULL:
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- __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__tempfile), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tempfile, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- * import sys
- * import types
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+ * '''number of :term:`filename` associated with this object.'''
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- * import sys # <<<<<<<<<<<<<<
- * import types
- * import itertools
+ /* "csamtools.pyx":328
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+ * if not self._isOpen():
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- * import types # <<<<<<<<<<<<<<
- * import itertools
- * import struct
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- * import struct
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- * import struct # <<<<<<<<<<<<<<
- * import ctypes
- * import collections
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+ * '''
+ * convert numerical :term:`tid` into :term:`reference` name.'''
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- * import collections
- * import re
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+ * '''
+ * convert numerical :term:`tid` into :term:`reference` name.'''
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- * import re
- * import platform
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- * import platform
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- * from cpython cimport PyErr_SetString
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+}
+
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+PyMODINIT_FUNC initcsamtools(void); /*proto*/
+PyMODINIT_FUNC initcsamtools(void)
+#else
+PyMODINIT_FUNC PyInit_csamtools(void); /*proto*/
+PyMODINIT_FUNC PyInit_csamtools(void)
+#endif
+{
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_4;
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+ __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #ifdef __pyx_binding_PyCFunctionType_USED
+ if (__pyx_binding_PyCFunctionType_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ /*--- Library function declarations ---*/
+ /*--- Threads initialization code ---*/
+ #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
+ #ifdef WITH_THREAD /* Python build with threading support? */
+ PyEval_InitThreads();
+ #endif
+ #endif
+ /*--- Module creation code ---*/
+ #if PY_MAJOR_VERSION < 3
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("csamtools"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
+ #else
+ __pyx_m = PyModule_Create(&__pyx_moduledef);
+ #endif
+ if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ #if PY_MAJOR_VERSION < 3
+ Py_INCREF(__pyx_m);
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+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
+ if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ /*--- Initialize various global constants etc. ---*/
+ if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_module_is_main_csamtools) {
+ if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+ /*--- Constants init code ---*/
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+ /*--- Function export code ---*/
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+ if (PyType_Ready(&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1932; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
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+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_9csamtools_11AlignedRead_2__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_11AlignedRead_2__str__.doc = __pyx_doc_9csamtools_11AlignedRead_2__str__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_11AlignedRead_2__str__;
+ }
+ }
+ if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1932; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_AlignedRead = &__pyx_type_9csamtools_AlignedRead;
+ __pyx_vtabptr_9csamtools_Samfile = &__pyx_vtable_9csamtools_Samfile;
+ __pyx_vtable_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_9csamtools_Samfile *, PyObject *))__pyx_f_9csamtools_7Samfile__buildHeader;
+ __pyx_vtable_9csamtools_Samfile.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_getCurrent;
+ __pyx_vtable_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_cnext;
+ __pyx_vtable_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_9csamtools_7Samfile_write;
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+ {
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+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
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+ __pyx_wrapperbase_9csamtools_7Samfile_21__next__.doc = __pyx_doc_9csamtools_7Samfile_21__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile_21__next__;
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+ if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_Samfile = &__pyx_type_9csamtools_Samfile;
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+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRow = &__pyx_type_9csamtools_IteratorRow;
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+ __pyx_vtable_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_cnext;
+ __pyx_type_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__.doc = __pyx_doc_9csamtools_14IteratorRowAll_2__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__;
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+ }
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowAll = &__pyx_type_9csamtools_IteratorRowAll;
+ if (PyType_Ready(&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_PileupProxy = &__pyx_type_9csamtools_PileupProxy;
+ if (PyType_Ready(&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_PileupRead = &__pyx_type_9csamtools_PileupRead;
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+ __pyx_vtable_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_9csamtools_9Fastafile__fetch;
+ if (PyType_Ready(&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_vtabptr_9csamtools_IteratorRowRegion = &__pyx_vtable_9csamtools_IteratorRowRegion;
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+ {
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+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
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+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowRegion = &__pyx_type_9csamtools_IteratorRowRegion;
+ __pyx_type_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
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+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
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+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__;
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+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_vtable_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_cnext;
+ __pyx_type_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_9csamtools_IteratorRow;
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+ {
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+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
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+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_vtable_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_setMask;
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+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __Pyx_GOTREF(__pyx_t_4);
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- __Pyx_GOTREF(__pyx_t_4);
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- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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+ * ):
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+ * catch_stdout = True,
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+ * # cython: profile=True
+ * # adds doc-strings for sphinx
+ */
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+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*
* cdef extern from "Python.h": # <<<<<<<<<<<<<<
* # The C structure of the objects used to describe built-in types.
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
if (__pyx_m) {
__Pyx_AddTraceback("init csamtools");
Py_DECREF(__pyx_m); __pyx_m = 0;
__pyx_empty_bytes /*PyObject *lnotab*/
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Py_XDECREF(py_srcfile);
Py_XDECREF(py_funcname);
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return py_code;
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return 0;
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- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+
+ tmp_type = tstate->curexc_type;
+ tmp_value = tstate->curexc_value;
+ tmp_tb = tstate->curexc_traceback;
+ tstate->curexc_type = type;
+ tstate->curexc_value = value;
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->curexc_type;
+ *value = tstate->curexc_value;
+ *tb = tstate->curexc_traceback;
+
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+}
+
+
+#if PY_MAJOR_VERSION < 3
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ Py_XINCREF(type);
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ /* First, check the traceback argument, replacing None with NULL. */
+ if (tb == Py_None) {
+ Py_DECREF(tb);
+ tb = 0;
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+ PyErr_SetString(PyExc_TypeError,
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+ goto raise_error;
+ }
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+ Py_INCREF(value);
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+ goto raise_error;
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+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
#else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AS_STRING(kw_name));
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
#endif
+ }
+
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
}
-static void __Pyx_RaiseArgtupleInvalid(
- const char* func_name,
- int exact,
- Py_ssize_t num_min,
- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
- const char *number, *more_or_less;
+#else /* Python 3+ */
- if (num_found < num_min) {
- num_expected = num_min;
- more_or_less = "at least";
- } else {
- num_expected = num_max;
- more_or_less = "at most";
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ if (tb == Py_None) {
+ tb = 0;
+ } else if (tb && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto bad;
}
- if (exact) {
- more_or_less = "exactly";
+ if (value == Py_None)
+ value = 0;
+
+ if (PyExceptionInstance_Check(type)) {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto bad;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(value);
+ } else if (!PyExceptionClass_Check(type)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto bad;
}
- number = (num_expected == 1) ? "" : "s";
- PyErr_Format(PyExc_TypeError,
- #if PY_VERSION_HEX < 0x02050000
- "%s() takes %s %d positional argument%s (%d given)",
+
+ PyErr_SetObject(type, value);
+
+ if (tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* tmp_tb = tstate->curexc_traceback;
+ if (tb != tmp_tb) {
+ Py_INCREF(tb);
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_tb);
+ }
+ }
+
+bad:
+ return;
+}
+#endif
+
+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name,
+ PyObject* kw_name)
+{
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION >= 3
+ "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
- "%s() takes %s %zd positional argument%s (%zd given)",
+ "%s() got multiple values for keyword argument '%s'", func_name,
+ PyString_AS_STRING(kw_name));
#endif
- func_name, more_or_less, num_expected, number, num_found);
}
static int __Pyx_ParseOptionalKeywords(
return -1;
}
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
-
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-}
-
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
+static void __Pyx_RaiseArgtupleInvalid(
+ const char* func_name,
+ int exact,
+ Py_ssize_t num_min,
+ Py_ssize_t num_max,
+ Py_ssize_t num_found)
+{
+ Py_ssize_t num_expected;
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- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
+ if (num_found < num_min) {
+ num_expected = num_min;
+ more_or_less = "at least";
+ } else {
+ num_expected = num_max;
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+ }
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+ PyErr_Format(PyExc_TypeError,
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+ "%s() takes %s %d positional argument%s (%d given)",
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+ "%s() takes %s %zd positional argument%s (%zd given)",
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}
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static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
const char *name, int exact)
{
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-
static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
}
return module;
}
-static PyObject *__Pyx_CreateClass(
- PyObject *bases, PyObject *dict, PyObject *name, const char *modname)
-{
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- PyObject *result = 0;
+static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
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+#if PY_MAJOR_VERSION < 3
+ if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
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+ Py_INCREF(metaclass);
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+}
- #if PY_MAJOR_VERSION < 3
- py_modname = PyString_FromString(modname);
- #else
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- goto bad;
- if (PyDict_SetItemString(dict, "__module__", py_modname) < 0)
- goto bad;
- #if PY_MAJOR_VERSION < 3
- result = PyClass_New(bases, dict, name);
- #else
- result = PyObject_CallFunctionObjArgs((PyObject *)&PyType_Type, name, bases, dict, NULL);
- #endif
-bad:
- Py_XDECREF(py_modname);
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
+ PyObject *modname) {
+ PyObject *result;
+ PyObject *metaclass;
+
+ if (PyDict_SetItemString(dict, "__module__", modname) < 0)
+ return NULL;
+
+ /* Python2 __metaclass__ */
+ metaclass = PyDict_GetItemString(dict, "__metaclass__");
+ if (metaclass) {
+ Py_INCREF(metaclass);
+ } else {
+ metaclass = __Pyx_FindPy2Metaclass(bases);
+ }
+ result = PyObject_CallFunctionObjArgs(metaclass, name, bases, dict, NULL);
+ Py_DECREF(metaclass);
return result;
}
+
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+ if (op == NULL)
+ return NULL;
+ op->func.m_ml = ml;
+ Py_XINCREF(self);
+ op->func.m_self = self;
+ Py_XINCREF(module);
+ op->func.m_module = module;
+ PyObject_GC_Track(op);
+ return (PyObject *)op;
+}
+
+static void __pyx_binding_PyCFunctionType_dealloc(__pyx_binding_PyCFunctionType_object *m) {
+ PyObject_GC_UnTrack(m);
+ Py_XDECREF(m->func.m_self);
+ Py_XDECREF(m->func.m_module);
+ PyObject_GC_Del(m);
+}
+
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+}
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+ __pyx_binding_PyCFunctionType_type.tp_name = __Pyx_NAMESTR("cython_binding_builtin_function_or_method");
+ __pyx_binding_PyCFunctionType_type.tp_dealloc = (destructor)__pyx_binding_PyCFunctionType_dealloc;
+ __pyx_binding_PyCFunctionType_type.tp_descr_get = __pyx_binding_PyCFunctionType_descr_get;
+ if (PyType_Ready(&__pyx_binding_PyCFunctionType_type) < 0) {
+ return -1;
+ }
+ __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type;
+ return 0;
+
+}
+
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
const int is_unsigned = const_zero < neg_one;
}
}
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- /* First, check the traceback argument, replacing None with NULL. */
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- /* Next, replace a missing value with None */
- if (value == NULL) {
- value = Py_None;
- Py_INCREF(value);
- }
- #if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
- #else
- if (!PyType_Check(type))
- #endif
- {
- /* Raising an instance. The value should be a dummy. */
- if (value != Py_None) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- /* Normalize to raise <class>, <instance> */
- Py_DECREF(value);
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
-
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-
-#else /* Python 3+ */
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
-
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
-
- PyErr_SetObject(type, value);
-
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-
-bad:
- return;
-}
-#endif
-
static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
const int is_unsigned = const_zero < neg_one;
}
}
-#if PY_MAJOR_VERSION < 3
-static PyObject *__Pyx_GetStdout(void) {
- PyObject *f = PySys_GetObject((char *)"stdout");
- if (!f) {
- PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout");
- }
- return f;
-}
-
-static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) {
- PyObject* v;
- int i;
-
- if (!f) {
- if (!(f = __Pyx_GetStdout()))
- return -1;
- }
- for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) {
- if (PyFile_SoftSpace(f, 1)) {
- if (PyFile_WriteString(" ", f) < 0)
- return -1;
- }
- v = PyTuple_GET_ITEM(arg_tuple, i);
- if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0)
- return -1;
- if (PyString_Check(v)) {
- char *s = PyString_AsString(v);
- Py_ssize_t len = PyString_Size(v);
- if (len > 0 &&
- isspace(Py_CHARMASK(s[len-1])) &&
- s[len-1] != ' ')
- PyFile_SoftSpace(f, 0);
- }
- }
- if (newline) {
- if (PyFile_WriteString("\n", f) < 0)
- return -1;
- PyFile_SoftSpace(f, 0);
- }
- return 0;
-}
-
-#else /* Python 3 has a print function */
-
-static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) {
- PyObject* kwargs = 0;
- PyObject* result = 0;
- PyObject* end_string;
- if (unlikely(!__pyx_print)) {
- __pyx_print = __Pyx_GetAttrString(__pyx_b, "print");
- if (!__pyx_print)
- return -1;
- }
- if (stream) {
- kwargs = PyDict_New();
- if (unlikely(!kwargs))
- return -1;
- if (unlikely(PyDict_SetItemString(kwargs, "file", stream) < 0))
- goto bad;
- if (!newline) {
- end_string = PyUnicode_FromStringAndSize(" ", 1);
- if (unlikely(!end_string))
- goto bad;
- if (PyDict_SetItemString(kwargs, "end", end_string) < 0) {
- Py_DECREF(end_string);
- goto bad;
- }
- Py_DECREF(end_string);
- }
- } else if (!newline) {
- if (unlikely(!__pyx_print_kwargs)) {
- __pyx_print_kwargs = PyDict_New();
- if (unlikely(!__pyx_print_kwargs))
- return -1;
- end_string = PyUnicode_FromStringAndSize(" ", 1);
- if (unlikely(!end_string))
- return -1;
- if (PyDict_SetItemString(__pyx_print_kwargs, "end", end_string) < 0) {
- Py_DECREF(end_string);
- return -1;
- }
- Py_DECREF(end_string);
- }
- kwargs = __pyx_print_kwargs;
- }
- result = PyObject_Call(__pyx_print, arg_tuple, kwargs);
- if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs))
- Py_DECREF(kwargs);
- if (!result)
- return -1;
- Py_DECREF(result);
- return 0;
-bad:
- if (kwargs != __pyx_print_kwargs)
- Py_XDECREF(kwargs);
- return -1;
-}
-
-#endif
-
-#if PY_MAJOR_VERSION < 3
-
-static int __Pyx_PrintOne(PyObject* f, PyObject *o) {
- if (!f) {
- if (!(f = __Pyx_GetStdout()))
- return -1;
- }
- if (PyFile_SoftSpace(f, 0)) {
- if (PyFile_WriteString(" ", f) < 0)
- return -1;
- }
- if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0)
- return -1;
- if (PyFile_WriteString("\n", f) < 0)
- return -1;
- return 0;
- /* the line below is just to avoid compiler
- * compiler warnings about unused functions */
- return __Pyx_Print(f, NULL, 0);
-}
-
-#else /* Python 3 has a print function */
-
-static int __Pyx_PrintOne(PyObject* stream, PyObject *o) {
- int res;
- PyObject* arg_tuple = PyTuple_New(1);
- if (unlikely(!arg_tuple))
- return -1;
- Py_INCREF(o);
- PyTuple_SET_ITEM(arg_tuple, 0, o);
- res = __Pyx_Print(stream, arg_tuple, 1);
- Py_DECREF(arg_tuple);
- return res;
-}
-
-#endif
-
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint64_t(uint64_t val) {
const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
const int is_unsigned = const_zero < neg_one;
if (!result)
goto bad;
if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
+ PyErr_Format(PyExc_TypeError,
"%s.%s is not a type object",
module_name, class_name);
goto bad;
}
if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
+ PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
#if PY_VERSION_HEX < 0x02050000
#endif
}
else if (((PyTypeObject *)result)->tp_basicsize != size) {
- PyErr_Format(PyExc_ValueError,
+ PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
goto bad;
char *text
ctypedef struct bam_index_t:
- pass
+ int32_t n
+ uint64_t n_no_coor
ctypedef struct bam_plbuf_t:
pass
void bam_plp_set_mask(bam_plp_t iter, int mask)
void bam_plp_reset(bam_plp_t iter)
void bam_plp_destroy(bam_plp_t iter)
+ void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt)
##################################################
int bam_cap_mapQ(bam1_t *b, char *ref, int thres)
-cdef extern from "glf.h":
- ctypedef struct glf1_t:
- pass
-
-cdef extern from "bam_maqcns.h":
-
- ctypedef struct bam_maqcns_t:
- float het_rate, theta
- int n_hap, cap_mapQ, errmod, min_baseQ
- float eta, q_r
- double *fk, *coef
- double *lhet
- void *aux
-
- glf1_t *bam_maqcns_glfgen(int n,
- bam_pileup1_t *pl,
- uint8_t ref_base,
- bam_maqcns_t *bm)
-
- ctypedef struct bam_maqindel_opt_t:
- int q_indel
- float r_indel
- float r_snp
- int mm_penalty, indel_err, ambi_thres
+#cdef extern from "glf.h":
+# ctypedef struct glf1_t:
+# pass
+
+#cdef extern from "bam_maqcns.h":
+#
+# ctypedef struct bam_maqcns_t:
+# float het_rate, theta
+# int n_hap, cap_mapQ, errmod, min_baseQ
+# float eta, q_r
+# double *fk, *coef
+# double *lhet
+# void *aux
+
+# glf1_t *bam_maqcns_glfgen(int n,
+# bam_pileup1_t *pl,
+# uint8_t ref_base,
+# bam_maqcns_t *bm)
+
+# ctypedef struct bam_maqindel_opt_t:
+# int q_indel
+# float r_indel
+# float r_snp
+# int mm_penalty, indel_err, ambi_thres
- uint32_t bam_maqcns_call(int n, bam_pileup1_t *pl, bam_maqcns_t *bm)
- bam_maqcns_t * bam_maqcns_init()
- void bam_maqcns_destroy(bam_maqcns_t *bm)
- void bam_maqcns_prepare(bam_maqcns_t *bm)
+# uint32_t bam_maqcns_call(int n, bam_pileup1_t *pl, bam_maqcns_t *bm)
+# bam_maqcns_t * bam_maqcns_init()
+# void bam_maqcns_destroy(bam_maqcns_t *bm)
+# void bam_maqcns_prepare(bam_maqcns_t *bm)
- uint32_t glf2cns(glf1_t *g, int q_r)
-
- int BAM_ERRMOD_MAQ2
- int BAM_ERRMOD_MAQ
- int BAM_ERRMOD_SOAP
-
- ctypedef struct bam_maqindel_ret_t:
- int indel1
- int indel2
- int cnt1
- int cnt2
- int cnt_anti
- int cnt_ref
- int cnt_ambi
- char *s[2]
- int gt
- int gl[2]
- int q_cns
- int q_ref
+# uint32_t glf2cns(glf1_t *g, int q_r)
+
+# int BAM_ERRMOD_MAQ2
+# int BAM_ERRMOD_MAQ
+# int BAM_ERRMOD_SOAP
+
+# ctypedef struct bam_maqindel_ret_t:
+# int indel1
+# int indel2
+# int cnt1
+# int cnt2
+# int cnt_anti
+# int cnt_ref
+# int cnt_ambi
+# char *s[2]
+# int gt
+# int gl[2]
+# int q_cns
+# int q_ref
- void bam_maqindel_ret_destroy( bam_maqindel_ret_t * )
+# void bam_maqindel_ret_destroy( bam_maqindel_ret_t * )
- bam_maqindel_opt_t *bam_maqindel_opt_init()
+# bam_maqindel_opt_t *bam_maqindel_opt_init()
- bam_maqindel_ret_t * bam_maqindel(int n,
- int pos,
- bam_maqindel_opt_t * mi,
- bam_pileup1_t * pl,
- char *ref,
- int _n_types,
- int * _types )
+# bam_maqindel_ret_t * bam_maqindel(int n,
+# int pos,
+# bam_maqindel_opt_t * mi,
+# bam_pileup1_t * pl,
+# char *ref,
+# int _n_types,
+# int * _types )
cdef extern from "faidx.h":
void pysam_set_stderr( FILE * file )
- uint32_t pysam_glf_depth( glf1_t * g )
+ # return mapped/unmapped reads on tid
+ uint32_t pysam_get_mapped( bam_index_t *idx, int tid )
+ uint32_t pysam_get_unmapped( bam_index_t *idx, int tid )
+
+# uint32_t pysam_glf_depth( glf1_t * g )
- void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c )
+# void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c )
# need to declare all C fields and methods here
cdef class AlignedRead:
cdef bam_index_t *index
# true if file is a bam file
cdef int isbam
+ # true if not a file but a stream
+ cdef int isstream
# true if file is not on the local filesystem
cdef int isremote
# current read within iteration
# file opening mode
cdef char * mode
+ # beginning of read section
+ cdef int64_t start_offset
+
cdef bam_header_t * _buildHeader( self, new_header )
cdef bam1_t * getCurrent( self )
cdef int cnext(self)
cdef char * _getrname( self, int tid )
+cdef class IteratorRow:
+ pass
+
+cdef class IteratorRowAll(IteratorRow):
+ cdef bam1_t * b
+ cdef samfile_t * fp
+ # true if samfile belongs to this object
+ cdef int owns_samfile
+
+ cdef bam1_t * getCurrent( self )
+
+ cdef int cnext(self)
+
+
cdef class Samfile:
- '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*
+ '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,
+ add_sq_text = False )*
A :term:`SAM`/:term:`BAM` formatted file. The file is automatically opened.
f = pysam.Samfile('ex1.bam','rb')
- If mode is not specified, we will try to auto-detect in the order 'r', 'rb', thus both the following
+ If mode is not specified, we will try to auto-detect in the order 'rb', 'r', thus both the following
should work::
f1 = pysam.Samfile('ex1.bam' )
- f2 = pysam.Samfile('ex1.bam' )
+ f2 = pysam.Samfile('ex1.sam' )
If an index for a BAM file exists (.bai), it will be opened automatically. Without an index random
access to reads via :meth:`fetch` and :meth:`pileup` is disabled.
3. If *text* is given, new header text is copied from raw text.
4. The names (*referencenames*) and lengths (*referencelengths*) are supplied directly as lists.
+ By default, 'SQ' and 'LN' tags will be added to the header text. This option can be
+ changed by unsetting the flag *add_sq_text*.
'''
self.samfile = NULL
self._filename = NULL
self.isbam = False
+ self.isstream = False
self._open( *args, **kwargs )
# allocate memory for iterator
text = None,
header = None,
port = None,
+ add_sq_text = True,
):
'''open a sam/bam file.
# read mode autodetection
if mode is None:
try:
- self._open(filename, 'r', template=template,
+ self._open(filename, 'rb', template=template,
referencenames=referencenames,
referencelengths=referencelengths,
text=text, header=header, port=port)
return
except ValueError, msg:
pass
- self._open(filename, 'rb', template=template,
+
+ self._open(filename, 'r', template=template,
referencenames=referencenames,
referencelengths=referencelengths,
text=text, header=header, port=port)
return
- assert mode in ( "r","w","rb","wb", "wh", "wbu" ), "invalid file opening mode `%s`" % mode
+ assert mode in ( "r","w","rb","wb", "wh", "wbu", "rU" ), "invalid file opening mode `%s`" % mode
assert filename != NULL
# close a previously opened file
if self._filename != NULL: free(self._filename )
self._filename = strdup( filename )
+ self.isstream = strcmp( filename, "-" ) == 0
self.isbam = len(mode) > 1 and mode[1] == 'b'
header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char))
strncpy( header_to_write.target_name[x], name, len(name) )
+ # Optionally, if there is no text, add a SAM compatible header to output
+ # file.
+ if text is None and add_sq_text:
+ text = ''
+ for x from 0 <= x < header_to_write.n_targets:
+ text += "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] )
+
if text != None:
# copy without \0
ctext = text
raise ValueError( "file does not have valid header (mode='%s') - is it SAM/BAM format?" % mode )
#disabled for autodetection to work
- if self.samfile.header.n_targets == 0:
- raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode)
+ # needs to be disabled so that reading from sam-files without headers works
+ #if self.samfile.header.n_targets == 0:
+ # raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode)
if self.samfile == NULL:
raise IOError("could not open file `%s`" % filename )
self.index = bam_index_load(filename)
if self.index == NULL:
raise IOError("error while opening index `%s` " % filename )
-
+
+ if not self.isstream:
+ self.start_offset = bam_tell( self.samfile.x.bam )
+
def gettid( self, reference ):
'''
convert :term:`reference` name into numerical :term:`tid`
return 1, rtid, rstart, rend
+ def reset( self ):
+ '''reset file position to beginning of read section.'''
+ return self.seek( self.start_offset, 0 )
+
def seek( self, uint64_t offset, int where = 0):
'''
move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.
raise ValueError( "I/O operation on closed file" )
if not self.isbam:
raise NotImplementedError("seek only available in bam files")
+ if self.isstream:
+ raise OSError("seek no available in streams")
+
return bam_seek( self.samfile.x.bam, offset, where )
def tell( self ):
:term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can
be supplied.
- Without *reference* or *region* all reads will be fetched. The reads will be returned
+ Without *reference* or *region* all mapped reads will be fetched. The reads will be returned
ordered by reference sequence, which will not necessarily be the order within the file.
+
If *until_eof* is given, all reads from the current file position will be returned
- *in order as they are within the file*.
+ in order as they are within the file. Using this option will also fetch unmapped reads.
If only *reference* is set, all reads aligned to *reference* will be fetched.
has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
+ if self.isstream: reopen = False
+ else: reopen = True
+
if self.isbam:
if not until_eof and not self._hasIndex() and not self.isremote:
raise ValueError( "fetch called on bamfile without index" )
fetch_callback )
else:
if has_coord:
- return IteratorRowRegion( self, rtid, rstart, rend )
+ return IteratorRowRegion( self, rtid, rstart, rend, reopen=reopen )
else:
if until_eof:
- return IteratorRowAll( self )
+ return IteratorRowAll( self, reopen=reopen )
else:
- return IteratorRowAllRefs(self)
+ # AH: check - reason why no reopen for AllRefs?
+ return IteratorRowAllRefs(self ) # , reopen=reopen )
else:
# check if header is present - otherwise sam_read1 aborts
# this happens if a bamfile is opened with mode 'r'
+ if has_coord:
+ raise ValueError ("fetching by region is not available for sam files" )
+
if self.samfile.header.n_targets == 0:
raise ValueError( "fetch called for samfile without header")
-
- if region != None:
- raise ValueError ("fetch for a region is not available for sam files" )
+
if callback:
raise NotImplementedError( "callback not implemented yet" )
else:
- return IteratorRowAll( self )
+ return IteratorRowAll( self, reopen=reopen )
def mate( self,
AlignedRead read ):
mask
Skip all reads with bits set in mask.
+ max_depth
+ Maximum read depth permitted. The default limit is *8000*.
.. note::
*all* reads which overlap the region are returned. The first base returned will be the
first base of the first read *not* necessarily the first base of the region used in the query.
- The maximum number of reads considered for pileup is *8000*. This limit is set by
- :term:`csamtools`.
-
'''
cdef int rtid, rstart, rend, has_coord
cdef bam_plbuf_t *buf
t.append( self.samfile.header.target_len[x] )
return tuple(t)
+ property mapped:
+ """total number of mapped reads in file.
+ """
+ def __get__(self):
+ if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
+
+ cdef int tid
+ cdef uint32_t total = 0
+ for tid from 0 <= tid < self.samfile.header.n_targets:
+ total += pysam_get_mapped( self.index, tid )
+ return total
+
+ property unmapped:
+ """total number of unmapped reads in file.
+ """
+ def __get__(self):
+ if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
+ cdef int tid
+ cdef uint32_t total = 0
+ for tid from 0 <= tid < self.samfile.header.n_targets:
+ total += pysam_get_unmapped( self.index, tid )
+ # get unmapped reads without coordinates
+ total += pysam_get_unmapped( self.index, -1 )
+ return total
+
property text:
'''full contents of the :term:`sam file` header as a string.'''
def __get__(self):
###############################################################
def __iter__(self):
if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ if not self.isbam and self.samfile.header.n_targets == 0:
+ raise NotImplementedError( "can not iterate over samfile without header")
return self
cdef bam1_t * getCurrent( self ):
to not re-open *samfile*.
"""
- cdef bam1_t * b
- cdef samfile_t * fp
- # true if samfile belongs to this object
- cdef int owns_samfile
+ # cdef bam1_t * b
+ # cdef samfile_t * fp
+ # # true if samfile belongs to this object
+ # cdef int owns_samfile
def __cinit__(self, Samfile samfile, int reopen = True ):
A :class:`FastaFile` object
mask
Skip all reads with bits set in mask.
-
-
+ max_depth
+ maximum read depth. The default is 8000.
'''
# result of the last plbuf_push
cdef Samfile samfile
cdef Fastafile fastafile
cdef stepper
+ cdef int max_depth
def __cinit__( self, Samfile samfile, **kwargs ):
self.samfile = samfile
self.mask = kwargs.get("mask", BAM_DEF_MASK )
self.fastafile = kwargs.get( "fastafile", None )
self.stepper = kwargs.get( "stepper", None )
+ self.max_depth = kwargs.get( "max_depth", 8000 )
self.iterdata.seq = NULL
self.tid = 0
self.pos = 0
self.plp = NULL
self.pileup_iter = <bam_plp_t>NULL
+
def __iter__(self):
return self
else:
raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper)
+ if self.max_depth:
+ bam_plp_set_maxcnt( self.pileup_iter, self.max_depth )
+
bam_plp_set_mask( self.pileup_iter, self.mask )
cdef reset( self, tid, start, end ):
read.tags = read.tags + [("RG",0)]
+
+ This method will happily write the same tag
+ multiple times.
"""
def __get__(self):
cdef char * ctag
cdef char auxtype
src = self._delegate
- if src.l_aux == 0: return None
+ if src.l_aux == 0: return []
s = bam1_aux( src )
result = []
'''length of the read (read only). Returns 0 if not given.'''
def __get__(self): return self._delegate.core.l_qseq
property aend:
- '''aligned end position of the read (read only). Returns
+ '''aligned end position of the read on the reference genome. Returns
None if not available.'''
def __get__(self):
cdef bam1_t * src
return None
return bam_calend(&src.core, bam1_cigar(src))
property alen:
- '''aligned length of the read (read only). Returns None if
+ '''aligned length of the read on the reference genome. Returns None if
not available.'''
def __get__(self):
cdef bam1_t * src
def __get__(self): return self._delegate.core.qual
def __set__(self, qual): self._delegate.core.qual = qual
property mrnm:
+ """the :term:`reference` id of the mate
+ deprecated, use RNEXT instead.
+ """
+ def __get__(self): return self._delegate.core.mtid
+ def __set__(self, mtid): self._delegate.core.mtid = mtid
+ property rnext:
"""the :term:`reference` id of the mate """
def __get__(self): return self._delegate.core.mtid
def __set__(self, mtid): self._delegate.core.mtid = mtid
property mpos:
+ """the position of the mate
+ deprecated, use PNEXT instead."""
+ def __get__(self): return self._delegate.core.mpos
+ def __set__(self, mpos): self._delegate.core.mpos = mpos
+ property pnext:
"""the position of the mate"""
def __get__(self): return self._delegate.core.mpos
def __set__(self, mpos): self._delegate.core.mpos = mpos
property isize:
+ """the insert size
+ deprecated: use tlen instead"""
+ def __get__(self): return self._delegate.core.isize
+ def __set__(self, isize): self._delegate.core.isize = isize
+ property tlen:
"""the insert size"""
def __get__(self): return self._delegate.core.isize
def __set__(self, isize): self._delegate.core.isize = isize
pos += l
return result
+
def overlap( self, uint32_t start, uint32_t end ):
- """return number of bases on reference overlapping *start* and *end*
+ """return number of aligned bases of read overlapping the interval *start* and *end*
+ on the reference sequence.
"""
cdef uint32_t k, i, pos, overlap
cdef int op, o
'''call ``method`` in samtools providing arguments in args.
.. note::
- This method redirects stdout and stderr to capture it
+ This method redirects stdout and (optionally) stderr to capture it
from samtools. If for some reason stdout/stderr disappears
the reason might be in this method.
'''
# note that debugging this module can be a problem
- # as stdout/stderr will not appear
-
+ # as stdout/stderr will not appear on the terminal
+
# some special cases
if method == "index":
if not os.path.exists( args[0] ):
if "-o" in args: raise ValueError("option -o is forbidden in samtools view")
args = ( "-o", stdout_f ) + args
-
# do the function call to samtools
cdef char ** cargs
cdef int i, n, retval
cargs[0] = "samtools"
cargs[1] = method
for i from 0 <= i < n: cargs[i+2] = args[i]
+
retval = pysam_dispatch(n+2, cargs)
free( cargs )
self.coverage ) ) )
-cdef class SNPCallerBase:
- '''Base class for SNP callers.
-
- *min_baseQ*
- minimum base quality (possibly capped by BAQ)
- *capQ_threshold*
- coefficient for adjusting mapQ of poor mappings
- *theta*
- theta in maq consensus calling model
- *n_haplotypes*
- number of haplotypes in the sample
- *het_rate*
- prior of a difference between two haplotypes
- '''
-
- cdef bam_maqcns_t * c
- cdef IteratorColumn iter
-
- def __cinit__(self,
- IteratorColumn iterator_column,
- **kwargs ):
-
- self.iter = iterator_column
- self.c = bam_maqcns_init()
-
- # set the default parameterization according to
- # samtools
-
- # new default mode for samtools >0.1.10
- self.c.errmod = kwargs.get( "errmod", BAM_ERRMOD_MAQ2 )
-
- self.c.min_baseQ = kwargs.get( "min_baseQ", 13 )
- # self.c.capQ_thres = kwargs.get( "capQ_threshold", 60 )
- self.c.n_hap = kwargs.get( "n_haplotypes", 2 )
- self.c.het_rate = kwargs.get( "het_rate", 0.001 )
- self.c.theta = kwargs.get( "theta", 0.83 )
-
- if self.c.errmod != BAM_ERRMOD_MAQ2:
- self.c.theta += 0.02
-
- # call prepare AFTER setting parameters
- bam_maqcns_prepare( self.c )
-
- def __dealloc__(self):
- bam_maqcns_destroy( self.c )
-
- cdef __dump( self, glf1_t * g, uint32_t cns, int rb ):
- '''debugging output.'''
-
- pysam_dump_glf( g, self.c );
- print ""
- for x in range(self.iter.n_plp):
- print "--> read %i %s %i" % (x,
- bam1_qname(self.iter.plp[x].b),
- self.iter.plp[x].qpos,
- )
-
- print "pos=%i, cns=%i, q_r = %f, depth=%i, n=%i, rb=%i, cns-cq=%i %i %i %i" \
- % (self.iter.pos,
- cns,
- self.c.q_r,
- self.iter.n_plp,
- self.iter.n_plp,
- rb,
- cns >> 8 & 0xff,
- cns >> 16 & 0xff,
- cns & 0xff,
- cns >> 28,
- )
-
- printf("-------------------------------------\n");
- sys.stdout.flush()
-
-cdef class IteratorSNPCalls( SNPCallerBase ):
- """*(IteratorColumn iterator)*
-
- call SNPs within a region.
-
- *iterator* is a pileup iterator. SNPs will be called
- on all positions returned by this iterator.
-
- This caller is fast if SNPs are called over large continuous
- regions. It is slow, if instantiated frequently and in random
- order as the sequence will have to be reloaded.
-
- """
+# cdef class SNPCallerBase:
+# '''Base class for SNP callers.
+
+# *min_baseQ*
+# minimum base quality (possibly capped by BAQ)
+# *capQ_threshold*
+# coefficient for adjusting mapQ of poor mappings
+# *theta*
+# theta in maq consensus calling model
+# *n_haplotypes*
+# number of haplotypes in the sample
+# *het_rate*
+# prior of a difference between two haplotypes
+# '''
+
+# cdef bam_maqcns_t * c
+# cdef IteratorColumn iter
+
+# def __cinit__(self,
+# IteratorColumn iterator_column,
+# **kwargs ):
+
+# self.iter = iterator_column
+# self.c = bam_maqcns_init()
+
+# # set the default parameterization according to
+# # samtools
+
+# # new default mode for samtools >0.1.10
+# self.c.errmod = kwargs.get( "errmod", BAM_ERRMOD_MAQ2 )
+
+# self.c.min_baseQ = kwargs.get( "min_baseQ", 13 )
+# # self.c.capQ_thres = kwargs.get( "capQ_threshold", 60 )
+# self.c.n_hap = kwargs.get( "n_haplotypes", 2 )
+# self.c.het_rate = kwargs.get( "het_rate", 0.001 )
+# self.c.theta = kwargs.get( "theta", 0.83 )
+
+# if self.c.errmod != BAM_ERRMOD_MAQ2:
+# self.c.theta += 0.02
+
+# # call prepare AFTER setting parameters
+# bam_maqcns_prepare( self.c )
+
+# def __dealloc__(self):
+# bam_maqcns_destroy( self.c )
+
+ # cdef __dump( self, glf1_t * g, uint32_t cns, int rb ):
+ # '''debugging output.'''
+
+ # pysam_dump_glf( g, self.c );
+ # print ""
+ # for x in range(self.iter.n_plp):
+ # print "--> read %i %s %i" % (x,
+ # bam1_qname(self.iter.plp[x].b),
+ # self.iter.plp[x].qpos,
+ # )
+
+ # print "pos=%i, cns=%i, q_r = %f, depth=%i, n=%i, rb=%i, cns-cq=%i %i %i %i" \
+ # % (self.iter.pos,
+ # cns,
+ # self.c.q_r,
+ # self.iter.n_plp,
+ # self.iter.n_plp,
+ # rb,
+ # cns >> 8 & 0xff,
+ # cns >> 16 & 0xff,
+ # cns & 0xff,
+ # cns >> 28,
+ # )
+
+ # printf("-------------------------------------\n");
+ # sys.stdout.flush()
+
+# cdef class IteratorSNPCalls( SNPCallerBase ):
+# """*(IteratorColumn iterator)*
+
+# call SNPs within a region.
+
+# *iterator* is a pileup iterator. SNPs will be called
+# on all positions returned by this iterator.
+
+# This caller is fast if SNPs are called over large continuous
+# regions. It is slow, if instantiated frequently and in random
+# order as the sequence will have to be reloaded.
+
+# """
- def __cinit__(self,
- IteratorColumn iterator_column,
- **kwargs ):
+# def __cinit__(self,
+# IteratorColumn iterator_column,
+# **kwargs ):
- assert self.iter.hasReference(), "IteratorSNPCalls requires an pileup iterator with reference sequence"
+# assert self.iter.hasReference(), "IteratorSNPCalls requires an pileup iterator with reference sequence"
- def __iter__(self):
- return self
+# def __iter__(self):
+# return self
- def __next__(self):
- """python version of next().
- """
+# def __next__(self):
+# """python version of next().
+# """
- # the following code was adapted from bam_plcmd.c:pileup_func()
- self.iter.cnext()
+# # the following code was adapted from bam_plcmd.c:pileup_func()
+# self.iter.cnext()
- if self.iter.n_plp < 0:
- raise ValueError("error during iteration" )
+# if self.iter.n_plp < 0:
+# raise ValueError("error during iteration" )
- if self.iter.plp == NULL:
- raise StopIteration
+# if self.iter.plp == NULL:
+# raise StopIteration
- cdef char * seq = self.iter.getSequence()
- cdef int seq_len = self.iter.seq_len
+# cdef char * seq = self.iter.getSequence()
+# cdef int seq_len = self.iter.seq_len
- assert seq != NULL
+# assert seq != NULL
- # reference base
- if self.iter.pos >= seq_len:
- raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) )
+# # reference base
+# if self.iter.pos >= seq_len:
+# raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) )
- cdef int rb = seq[self.iter.pos]
- cdef uint32_t cns
- cdef glf1_t * g
+# cdef int rb = seq[self.iter.pos]
+# cdef uint32_t cns
+# cdef glf1_t * g
- g = bam_maqcns_glfgen( self.iter.n_plp,
- self.iter.plp,
- bam_nt16_table[rb],
- self.c )
+# g = bam_maqcns_glfgen( self.iter.n_plp,
+# self.iter.plp,
+# bam_nt16_table[rb],
+# self.c )
- if pysam_glf_depth( g ) == 0:
- cns = 0xfu << 28 | 0xf << 24
- else:
- cns = glf2cns(g, <int>(self.c.q_r + .499))
-
- free(g)
+# if pysam_glf_depth( g ) == 0:
+# cns = 0xfu << 28 | 0xf << 24
+# else:
+# cns = glf2cns(g, <int>(self.c.q_r + .499))
+
+# free(g)
- cdef SNPCall call
+# cdef SNPCall call
- call = SNPCall()
- call._tid = self.iter.tid
- call._pos = self.iter.pos
- call._reference_base = rb
- call._genotype = bam_nt16_rev_table[cns>>28]
- call._consensus_quality = cns >> 8 & 0xff
- call._snp_quality = cns & 0xff
- call._rms_mapping_quality = cns >> 16&0xff
- call._coverage = self.iter.n_plp
+# call = SNPCall()
+# call._tid = self.iter.tid
+# call._pos = self.iter.pos
+# call._reference_base = rb
+# call._genotype = bam_nt16_rev_table[cns>>28]
+# call._consensus_quality = cns >> 8 & 0xff
+# call._snp_quality = cns & 0xff
+# call._rms_mapping_quality = cns >> 16&0xff
+# call._coverage = self.iter.n_plp
- return call
+# return call
-cdef class SNPCaller( SNPCallerBase ):
- '''*(IteratorColumn iterator_column )*
+# cdef class SNPCaller( SNPCallerBase ):
+# '''*(IteratorColumn iterator_column )*
- The samtools SNP caller.
+# The samtools SNP caller.
- This object will call SNPs in *samfile* against the reference
- sequence in *fasta*.
+# This object will call SNPs in *samfile* against the reference
+# sequence in *fasta*.
- This caller is fast for calling few SNPs in selected regions.
+# This caller is fast for calling few SNPs in selected regions.
- It is slow, if called over large genomic regions.
- '''
+# It is slow, if called over large genomic regions.
+# '''
- def __cinit__(self,
- IteratorColumn iterator_column,
- **kwargs ):
+# def __cinit__(self,
+# IteratorColumn iterator_column,
+# **kwargs ):
- pass
+# pass
- def call(self, reference, int pos ):
- """call a snp on chromosome *reference*
- and position *pos*.
+# def call(self, reference, int pos ):
+# """call a snp on chromosome *reference*
+# and position *pos*.
- returns a :class:`SNPCall` object.
- """
+# returns a :class:`SNPCall` object.
+# """
- cdef int tid = self.iter.samfile.gettid( reference )
+# cdef int tid = self.iter.samfile.gettid( reference )
- self.iter.reset( tid, pos, pos + 1 )
+# self.iter.reset( tid, pos, pos + 1 )
- while 1:
- self.iter.cnext()
+# while 1:
+# self.iter.cnext()
- if self.iter.n_plp < 0:
- raise ValueError("error during iteration" )
+# if self.iter.n_plp < 0:
+# raise ValueError("error during iteration" )
- if self.iter.plp == NULL:
- raise ValueError( "no reads in region - no call" )
+# if self.iter.plp == NULL:
+# raise ValueError( "no reads in region - no call" )
- if self.iter.pos == pos: break
-
- cdef char * seq = self.iter.getSequence()
- cdef int seq_len = self.iter.seq_len
-
- assert seq != NULL
-
- # reference base
- if self.iter.pos >= seq_len:
- raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) )
-
- cdef int rb = seq[self.iter.pos]
- cdef uint32_t cns
- cdef glf1_t * g
-
- g = bam_maqcns_glfgen( self.iter.n_plp,
- self.iter.plp,
- bam_nt16_table[rb],
- self.c )
-
-
- if pysam_glf_depth( g ) == 0:
- cns = 0xfu << 28 | 0xf << 24
- else:
- cns = glf2cns(g, <int>(self.c.q_r + .499))
-
- free(g)
+# if self.iter.pos == pos: break
+
+# cdef char * seq = self.iter.getSequence()
+# cdef int seq_len = self.iter.seq_len
+
+# assert seq != NULL
+
+# # reference base
+# if self.iter.pos >= seq_len:
+# raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) )
+
+# cdef int rb = seq[self.iter.pos]
+# cdef uint32_t cns
+# # cdef glf1_t * g
+# #
+# # g = bam_maqcns_glfgen( self.iter.n_plp,
+# # self.iter.plp,
+# # bam_nt16_table[rb],
+# # self.c )
+# ##
+# #
+# # if pysam_glf_depth( g ) == 0:
+# # cns = 0xfu << 28 | 0xf << 24
+# # else:
+# # cns = glf2cns(g, <int>(self.c.q_r + .499))
+# #
+# # free(g)
- cdef SNPCall call
-
- call = SNPCall()
- call._tid = self.iter.tid
- call._pos = self.iter.pos
- call._reference_base = rb
- call._genotype = bam_nt16_rev_table[cns>>28]
- call._consensus_quality = cns >> 8 & 0xff
- call._snp_quality = cns & 0xff
- call._rms_mapping_quality = cns >> 16&0xff
- call._coverage = self.iter.n_plp
-
- return call
-
-cdef class IndelCall:
- '''the results of an indel call.'''
- cdef int _tid
- cdef int _pos
- cdef int _coverage
- cdef int _rms_mapping_quality
- cdef bam_maqindel_ret_t * _r
-
- def __cinit__(self):
- #assert r != NULL
- #self._r = r
- pass
-
- property tid:
- '''the chromosome ID as is defined in the header'''
- def __get__(self):
- return self._tid
+# cdef SNPCall call
+
+# call = SNPCall()
+# call._tid = self.iter.tid
+# call._pos = self.iter.pos
+# call._reference_base = rb
+# call._genotype = bam_nt16_rev_table[cns>>28]
+# call._consensus_quality = cns >> 8 & 0xff
+# call._snp_quality = cns & 0xff
+# call._rms_mapping_quality = cns >> 16&0xff
+# call._coverage = self.iter.n_plp
+
+# return call
+
+# cdef class IndelCall:
+# '''the results of an indel call.'''
+# cdef int _tid
+# cdef int _pos
+# cdef int _coverage
+# cdef int _rms_mapping_quality
+# cdef bam_maqindel_ret_t * _r
+
+# def __cinit__(self):
+# #assert r != NULL
+# #self._r = r
+# pass
+
+# property tid:
+# '''the chromosome ID as is defined in the header'''
+# def __get__(self):
+# return self._tid
- property pos:
- '''nucleotide position of SNP.'''
- def __get__(self): return self._pos
-
- property genotype:
- '''the genotype called.'''
- def __get__(self):
- if self._r.gt == 0:
- s = PyString_FromStringAndSize( self._r.s[0], self._r.indel1 + 1)
- return "%s/%s" % (s,s)
- elif self._r.gt == 1:
- s = PyString_FromStringAndSize( self._r.s[1], self._r.indel2 + 1)
- return "%s/%s" % (s,s)
- else:
- return "%s/%s" % (self.first_allele, self.second_allele )
-
- property consensus_quality:
- '''the genotype quality (Phred-scaled).'''
- def __get__(self): return self._r.q_cns
-
- property snp_quality:
- '''the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.'''
- def __get__(self): return self._r.q_ref
-
- property mapping_quality:
- '''the root mean square (rms) of the mapping quality of all reads involved in the call.'''
- def __get__(self): return self._rms_mapping_quality
-
- property coverage:
- '''coverage or read depth - the number of reads involved in the call.'''
- def __get__(self): return self._coverage
-
- property first_allele:
- '''sequence of first allele.'''
- def __get__(self): return PyString_FromStringAndSize( self._r.s[0], self._r.indel1 + 1)
-
- property second_allele:
- '''sequence of second allele.'''
- def __get__(self): return PyString_FromStringAndSize( self._r.s[1], self._r.indel2 + 1)
-
- property reads_first:
- '''reads supporting first allele.'''
- def __get__(self): return self._r.cnt1
-
- property reads_second:
- '''reads supporting first allele.'''
- def __get__(self): return self._r.cnt2
-
- property reads_diff:
- '''reads supporting first allele.'''
- def __get__(self): return self._r.cnt_anti
-
- def __str__(self):
-
- return "\t".join( map(str, (
- self.tid,
- self.pos,
- self.genotype,
- self.consensus_quality,
- self.snp_quality,
- self.mapping_quality,
- self.coverage,
- self.first_allele,
- self.second_allele,
- self.reads_first,
- self.reads_second,
- self.reads_diff ) ) )
-
- def __dealloc__(self ):
- bam_maqindel_ret_destroy(self._r)
-
-cdef class IndelCallerBase:
- '''Base class for SNP callers.
-
- *min_baseQ*
- minimum base quality (possibly capped by BAQ)
- *capQ_threshold*
- coefficient for adjusting mapQ of poor mappings
- *theta*
- theta in maq consensus calling model
- *n_haplotypes*
- number of haplotypes in the sample
- *het_rate*
- prior of a difference between two haplotypes
- '''
-
- cdef bam_maqindel_opt_t * options
- cdef IteratorColumn iter
- cdef int cap_mapQ
- cdef int max_depth
-
- def __cinit__(self,
- IteratorColumn iterator_column,
- **kwargs ):
+# property pos:
+# '''nucleotide position of SNP.'''
+# def __get__(self): return self._pos
+
+# property genotype:
+# '''the genotype called.'''
+# def __get__(self):
+# if self._r.gt == 0:
+# s = PyString_FromStringAndSize( self._r.s[0], self._r.indel1 + 1)
+# return "%s/%s" % (s,s)
+# elif self._r.gt == 1:
+# s = PyString_FromStringAndSize( self._r.s[1], self._r.indel2 + 1)
+# return "%s/%s" % (s,s)
+# else:
+# return "%s/%s" % (self.first_allele, self.second_allele )
+
+# property consensus_quality:
+# '''the genotype quality (Phred-scaled).'''
+# def __get__(self): return self._r.q_cns
+
+# property snp_quality:
+# '''the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.'''
+# def __get__(self): return self._r.q_ref
+
+# property mapping_quality:
+# '''the root mean square (rms) of the mapping quality of all reads involved in the call.'''
+# def __get__(self): return self._rms_mapping_quality
+
+# property coverage:
+# '''coverage or read depth - the number of reads involved in the call.'''
+# def __get__(self): return self._coverage
+
+# property first_allele:
+# '''sequence of first allele.'''
+# def __get__(self): return PyString_FromStringAndSize( self._r.s[0], self._r.indel1 + 1)
+
+# property second_allele:
+# '''sequence of second allele.'''
+# def __get__(self): return PyString_FromStringAndSize( self._r.s[1], self._r.indel2 + 1)
+
+# property reads_first:
+# '''reads supporting first allele.'''
+# def __get__(self): return self._r.cnt1
+
+# property reads_second:
+# '''reads supporting first allele.'''
+# def __get__(self): return self._r.cnt2
+
+# property reads_diff:
+# '''reads supporting first allele.'''
+# def __get__(self): return self._r.cnt_anti
+
+# def __str__(self):
+
+# return "\t".join( map(str, (
+# self.tid,
+# self.pos,
+# self.genotype,
+# self.consensus_quality,
+# self.snp_quality,
+# self.mapping_quality,
+# self.coverage,
+# self.first_allele,
+# self.second_allele,
+# self.reads_first,
+# self.reads_second,
+# self.reads_diff ) ) )
+
+# def __dealloc__(self ):
+# bam_maqindel_ret_destroy(self._r)
+
+# cdef class IndelCallerBase:
+# '''Base class for SNP callers.
+
+# *min_baseQ*
+# minimum base quality (possibly capped by BAQ)
+# *capQ_threshold*
+# coefficient for adjusting mapQ of poor mappings
+# *theta*
+# theta in maq consensus calling model
+# *n_haplotypes*
+# number of haplotypes in the sample
+# *het_rate*
+# prior of a difference between two haplotypes
+# '''
+
+# cdef bam_maqindel_opt_t * options
+# cdef IteratorColumn iter
+# cdef int cap_mapQ
+# cdef int max_depth
+
+# def __cinit__(self,
+# IteratorColumn iterator_column,
+# **kwargs ):
+
+
+# self.iter = iterator_column
+
+# assert iterator_column.hasReference(), "IndelCallerBase requires an pileup iterator with reference sequence"
+
+# self.options = bam_maqindel_opt_init()
+
+# # set the default parameterization according to
+# # samtools
+
+# self.options.r_indel = kwargs.get( "r_indel", 0.00015 )
+# self.options.q_indel = kwargs.get( "q_indel", 40 )
+# self.cap_mapQ = kwargs.get( "cap_mapQ", 60 )
+# self.max_depth = kwargs.get( "max_depth", 1024 )
+
+# def __dealloc__(self):
+# free( self.options )
+# def _call( self ):
- self.iter = iterator_column
+# cdef char * seq = self.iter.getSequence()
+# cdef int seq_len = self.iter.seq_len
- assert iterator_column.hasReference(), "IndelCallerBase requires an pileup iterator with reference sequence"
-
- self.options = bam_maqindel_opt_init()
-
- # set the default parameterization according to
- # samtools
-
- self.options.r_indel = kwargs.get( "r_indel", 0.00015 )
- self.options.q_indel = kwargs.get( "q_indel", 40 )
- self.cap_mapQ = kwargs.get( "cap_mapQ", 60 )
- self.max_depth = kwargs.get( "max_depth", 1024 )
-
- def __dealloc__(self):
- free( self.options )
+# assert seq != NULL
- def _call( self ):
+# # reference base
+# if self.iter.pos >= seq_len:
+# raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) )
- cdef char * seq = self.iter.getSequence()
- cdef int seq_len = self.iter.seq_len
+# cdef bam_maqindel_ret_t * r
+
+# cdef int m = min( self.max_depth, self.iter.n_plp )
+
+# # printf("pysam: m=%i, q_indel=%i, r_indel=%f, r_snp=%i, mm_penalty=%i, indel_err=%i, ambi_thres=%i\n",
+# # m, self.options.q_indel, self.options.r_indel, self.options.r_snp, self.options.mm_penalty,
+# # self.options.indel_err, self.options.ambi_thres );
+
+# r = bam_maqindel(m,
+# self.iter.pos,
+# self.options,
+# self.iter.plp,
+# seq,
+# 0,
+# NULL)
+
+# if r == NULL: return None
- assert seq != NULL
+# cdef IndelCall call
+# call = IndelCall()
+# call._r = r
+# call._tid = self.iter.tid
+# call._pos = self.iter.pos
+# call._coverage = self.iter.n_plp
- # reference base
- if self.iter.pos >= seq_len:
- raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) )
+# cdef uint64_t rms_aux = 0
+# cdef int i = 0
+# cdef bam_pileup1_t * p
+# cdef int tmp
- cdef bam_maqindel_ret_t * r
-
- cdef int m = min( self.max_depth, self.iter.n_plp )
-
- # printf("pysam: m=%i, q_indel=%i, r_indel=%f, r_snp=%i, mm_penalty=%i, indel_err=%i, ambi_thres=%i\n",
- # m, self.options.q_indel, self.options.r_indel, self.options.r_snp, self.options.mm_penalty,
- # self.options.indel_err, self.options.ambi_thres );
-
- r = bam_maqindel(m,
- self.iter.pos,
- self.options,
- self.iter.plp,
- seq,
- 0,
- NULL)
-
- if r == NULL: return None
-
- cdef IndelCall call
- call = IndelCall()
- call._r = r
- call._tid = self.iter.tid
- call._pos = self.iter.pos
- call._coverage = self.iter.n_plp
-
- cdef uint64_t rms_aux = 0
- cdef int i = 0
- cdef bam_pileup1_t * p
- cdef int tmp
-
- for i from 0 <= i < self.iter.n_plp:
- p = self.iter.plp + i
- if p.b.core.qual < self.cap_mapQ:
- tmp = p.b.core.qual
- else:
- tmp = self.cap_mapQ
- rms_aux += tmp * tmp
+# for i from 0 <= i < self.iter.n_plp:
+# p = self.iter.plp + i
+# if p.b.core.qual < self.cap_mapQ:
+# tmp = p.b.core.qual
+# else:
+# tmp = self.cap_mapQ
+# rms_aux += tmp * tmp
- call._rms_mapping_quality = <uint64_t>(sqrt(<double>rms_aux / self.iter.n_plp) + .499)
+# call._rms_mapping_quality = <uint64_t>(sqrt(<double>rms_aux / self.iter.n_plp) + .499)
- return call
+# return call
-cdef class IndelCaller( IndelCallerBase ):
- '''*(IteratorColumn iterator_column )*
+# cdef class IndelCaller( IndelCallerBase ):
+# '''*(IteratorColumn iterator_column )*
- The samtools SNP caller.
+# The samtools SNP caller.
- This object will call SNPs in *samfile* against the reference
- sequence in *fasta*.
+# This object will call SNPs in *samfile* against the reference
+# sequence in *fasta*.
- This caller is fast for calling few SNPs in selected regions.
+# This caller is fast for calling few SNPs in selected regions.
- It is slow, if called over large genomic regions.
- '''
+# It is slow, if called over large genomic regions.
+# '''
- def __cinit__(self,
- IteratorColumn iterator_column,
- **kwargs ):
+# def __cinit__(self,
+# IteratorColumn iterator_column,
+# **kwargs ):
- pass
+# pass
- def call(self, reference, int pos ):
- """call a snp on chromosome *reference*
- and position *pos*.
+# def call(self, reference, int pos ):
+# """call a snp on chromosome *reference*
+# and position *pos*.
- returns a :class:`SNPCall` object or None, if no indel call could be made.
- """
+# returns a :class:`SNPCall` object or None, if no indel call could be made.
+# """
- cdef int tid = self.iter.samfile.gettid( reference )
+# cdef int tid = self.iter.samfile.gettid( reference )
- self.iter.reset( tid, pos, pos + 1 )
+# self.iter.reset( tid, pos, pos + 1 )
- while 1:
- self.iter.cnext()
+# while 1:
+# self.iter.cnext()
- if self.iter.n_plp < 0:
- raise ValueError("error during iteration" )
+# if self.iter.n_plp < 0:
+# raise ValueError("error during iteration" )
- if self.iter.plp == NULL:
- raise ValueError( "no reads in region - no call" )
+# if self.iter.plp == NULL:
+# raise ValueError( "no reads in region - no call" )
- if self.iter.pos == pos: break
+# if self.iter.pos == pos: break
- return self._call()
+# return self._call()
-cdef class IteratorIndelCalls( IndelCallerBase ):
- """*(IteratorColumn iterator)*
+# cdef class IteratorIndelCalls( IndelCallerBase ):
+# """*(IteratorColumn iterator)*
- call indels within a region.
+# call indels within a region.
- *iterator* is a pileup iterator. SNPs will be called
- on all positions returned by this iterator.
+# *iterator* is a pileup iterator. SNPs will be called
+# on all positions returned by this iterator.
- This caller is fast if SNPs are called over large continuous
- regions. It is slow, if instantiated frequently and in random
- order as the sequence will have to be reloaded.
+# This caller is fast if SNPs are called over large continuous
+# regions. It is slow, if instantiated frequently and in random
+# order as the sequence will have to be reloaded.
- """
+# """
- def __cinit__(self,
- IteratorColumn iterator_column,
- **kwargs ):
- pass
+# def __cinit__(self,
+# IteratorColumn iterator_column,
+# **kwargs ):
+# pass
- def __iter__(self):
- return self
+# def __iter__(self):
+# return self
- def __next__(self):
- """python version of next().
- """
+# def __next__(self):
+# """python version of next().
+# """
- # the following code was adapted from bam_plcmd.c:pileup_func()
- self.iter.cnext()
+# # the following code was adapted from bam_plcmd.c:pileup_func()
+# self.iter.cnext()
- if self.iter.n_plp < 0:
- raise ValueError("error during iteration" )
+# if self.iter.n_plp < 0:
+# raise ValueError("error during iteration" )
- if self.iter.plp == NULL:
- raise StopIteration
+# if self.iter.plp == NULL:
+# raise StopIteration
- return self._call()
+# return self._call()
"PileupColumn",
"PileupProxy",
"PileupRead",
- "IteratorSNPCalls",
- "SNPCaller",
- "IndelCaller",
- "IteratorIndelCalls",
+ # "IteratorSNPCalls",
+ # "SNPCaller",
+ # "IndelCaller",
+ # "IteratorIndelCalls",
"IndexedReads" ]
-/* Generated by Cython 0.13 on Thu May 5 14:57:46 2011 */
+/* Generated by Cython 0.14.1 on Fri Nov 25 20:32:50 2011 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#define PyBytes_Repr PyString_Repr
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
+#endif
+
+#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#endif
-
#ifndef PySet_CheckExact
-# define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
+ #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
+#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+
#if PY_MAJOR_VERSION >= 3
+ #define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
#define PyInt_Check(op) PyLong_Check(op)
#define PyInt_CheckExact(op) PyLong_CheckExact(op)
#endif
#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
+ #define PyBoolObject PyLongObject
#endif
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
#endif
+#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
+ #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
+ #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
+#else
+ #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
+ #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
+#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
#include "tabix.h"
#include "pythread.h"
+#ifdef PYREX_WITHOUT_ASSERTIONS
+#define CYTHON_WITHOUT_ASSERTIONS
+#endif
+
+
/* inline attribute */
#ifndef CYTHON_INLINE
#if defined(__GNUC__)
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
#define CYTHON_INLINE inline
#else
- #define CYTHON_INLINE
+ #define CYTHON_INLINE
#endif
#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
# endif
# elif defined(__ICC) || defined(__INTEL_COMPILER)
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
-# define CYTHON_UNUSED
+# define CYTHON_UNUSED
# endif
#endif
#ifdef __GNUC__
/* Test for GCC > 2.95 */
-#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
+#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
#define likely(x) __builtin_expect(!!(x), 1)
#define unlikely(x) __builtin_expect(!!(x), 0)
#else /* __GNUC__ > 2 ... */
static const char *__pyx_f[] = {
"ctabix.pyx",
"bool.pxd",
+ "complex.pxd",
"TabProxies.pxd",
};
/* Type declarations */
-/* "pysam/ctabix.pxd":178
+/* "ctabix.pxd":178
* cdef tabix_t * tabixfile
*
* cdef class Parser: # <<<<<<<<<<<<<<
PyObject_HEAD
};
-/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":293
+/* "ctabix.pyx":389
* return r
*
* cdef class asVCF( Parser ): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a VCF record.'''
- * def __call__(self, char * buffer, int len ):
+ * '''converts a :term:`tabix row` into a VCF record with
+ * the following fields:
*/
struct __pyx_obj_6ctabix_asVCF {
struct __pyx_obj_6ctabix_Parser __pyx_base;
};
-/* "pysam/TabProxies.pxd":42
+/* "TabProxies.pxd":42
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
int is_modified;
};
-/* "pysam/TabProxies.pxd":77
+/* "TabProxies.pxd":78
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
};
-/* "pysam/TabProxies.pxd":80
+/* "TabProxies.pxd":81
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
int bedfields;
};
-/* "pysam/TabProxies.pxd":91
+/* "TabProxies.pxd":92
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
uint32_t pos;
};
-/* "pysam/TabProxies.pxd":60
+/* "TabProxies.pxd":61
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
int hasOwnAttributes;
};
-/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":161
- * return result
+/* "ctabix.pyx":193
+ * if self._filename != NULL: free( self._filename )
*
* cdef class TabixIterator: # <<<<<<<<<<<<<<
* """iterates over rows in *tabixfile* in region
tabix_t *tabixfile;
};
-/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":304
+/* "ctabix.pyx":428
* #########################################################
* #########################################################
* cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
struct __pyx_obj_6ctabix_Parser *parser;
};
-/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":216
+/* "ctabix.pyx":248
* ti_iter_destroy(self.iterator)
*
* cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
tabix_t *tabixfile;
};
-/* "pysam/ctabix.pxd":172
+/* "ctabix.pxd":172
* # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
*
* cdef class Tabixfile: # <<<<<<<<<<<<<<
- * cdef char * filename
+ * cdef char * _filename
*
*/
struct __pyx_obj_6ctabix_Tabixfile {
PyObject_HEAD
- char *filename;
+ char *_filename;
tabix_t *tabixfile;
};
-/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":277
+/* "ctabix.pyx":312
* return r
*
* cdef class asGTF(Parser): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a GTF record.'''
- * def __call__(self, char * buffer, int len):
+ * '''converts a :term:`tabix row` into a GTF record with the following
+ * fields:
*/
struct __pyx_obj_6ctabix_asGTF {
struct __pyx_obj_6ctabix_Parser __pyx_base;
};
-/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":285
+/* "ctabix.pyx":349
* return r
*
* cdef class asBed( Parser ): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a GTF record.'''
- * def __call__(self, char * buffer, int len):
+ * '''converts a :term:`tabix row` into a bed record
+ * with the following fields:
*/
struct __pyx_obj_6ctabix_asBed {
struct __pyx_obj_6ctabix_Parser __pyx_base;
};
-/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":267
+/* "ctabix.pyx":299
* pass
*
* cdef class asTuple(Parser): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a python tuple.'''
- * def __call__(self, char * buffer, int len):
+ * '''converts a :term:`tabix row` into a python tuple.
+ *
*/
struct __pyx_obj_6ctabix_asTuple {
};
-/* "pysam/TabProxies.pxd":42
+/* "TabProxies.pxd":42
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
-/* "pysam/TabProxies.pxd":77
+/* "TabProxies.pxd":78
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
-/* "pysam/TabProxies.pxd":91
+/* "TabProxies.pxd":92
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
-/* "pysam/TabProxies.pxd":80
+/* "TabProxies.pxd":81
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
-/* "pysam/TabProxies.pxd":60
+/* "TabProxies.pxd":61
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
static void __Pyx_RaiseDoubleKeywordsError(
const char* func_name, PyObject* kw_name); /*proto*/
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
+
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
-
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
PyObject *r;
return r;
}
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
-
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-static int __Pyx_GetVtable(PyObject *dict, void *vtabptr); /*proto*/
+static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
static void __Pyx_AddTraceback(const char *funcname); /*proto*/
/* Module declarations from cpython.float */
+/* Module declarations from __builtin__ */
+
/* Module declarations from cpython.complex */
+static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
/* Module declarations from cpython.string */
/* Module declarations from cpython.unicode */
static PyTypeObject *__pyx_ptype_6ctabix_asVCF = 0;
static PyTypeObject *__pyx_ptype_6ctabix_TabixIteratorParsed = 0;
#define __Pyx_MODULE_NAME "ctabix"
-int __pyx_module_is_main_ctabix = 0;
+static int __pyx_module_is_main_ctabix = 0;
/* Implementation of ctabix */
static PyObject *__pyx_builtin_IOError;
static char __pyx_k_9[] = "start out of range (%i)";
static char __pyx_k_10[] = "end out of range (%i)";
static char __pyx_k_11[] = "I/O operation on closed file";
-static char __pyx_k_12[] = "malformatted query or wrong sequence name.\n";
-static char __pyx_k_13[] = "can't open header.\n";
-static char __pyx_k_15[] = "Filename '%s' already exists, use *force* to overwrite";
-static char __pyx_k_16[] = "could not open '%s' for writing";
-static char __pyx_k_17[] = "could not open '%s' for reading";
-static char __pyx_k_18[] = "writing failed";
-static char __pyx_k_20[] = "#";
-static char __pyx_k_22[] = "No such file '%s'";
-static char __pyx_k_23[] = ".gz";
-static char __pyx_k_24[] = "Filename '%s.tbi' already exists, use *force* to overwrite";
-static char __pyx_k_25[] = "unknown preset '%s', valid presets are '%s'";
-static char __pyx_k_26[] = ",";
-static char __pyx_k_27[] = "chromosome names";
-static char __pyx_k_28[] = "Tabixfile._isOpen (line 19)";
-static char __pyx_k_29[] = "Tabixfile._open (line 23)";
-static char __pyx_k_30[] = "Tabixfile._parseRegion (line 57)";
-static char __pyx_k_31[] = "Tabixfile.fetch (line 102)";
-static char __pyx_k_32[] = "Tabixfile.header.__get__ (line 140)";
-static char __pyx_k_33[] = "TabixIterator.__next__ (line 192)";
-static char __pyx_k_34[] = "TabixHeaderIterator.__next__ (line 239)";
-static char __pyx_k_35[] = "TabixIteratorParsed.__next__ (line 342)";
-static char __pyx_k_36[] = "tabix_compress (line 362)";
-static char __pyx_k_37[] = "tabix_index (line 407)";
+static char __pyx_k_14[] = "malformatted query or wrong sequence name.\n";
+static char __pyx_k_16[] = "can't open header.\n";
+static char __pyx_k_20[] = "Filename '%s' already exists, use *force* to overwrite";
+static char __pyx_k_21[] = "could not open '%s' for writing";
+static char __pyx_k_23[] = "could not open '%s' for reading";
+static char __pyx_k_25[] = "writing failed";
+static char __pyx_k_29[] = "#";
+static char __pyx_k_31[] = "No such file '%s'";
+static char __pyx_k_32[] = ".gz";
+static char __pyx_k_34[] = "Filename '%s.tbi' already exists, use *force* to overwrite";
+static char __pyx_k_42[] = "unknown preset '%s', valid presets are '%s'";
+static char __pyx_k_43[] = ",";
+static char __pyx_k_44[] = "filename associated with this object.";
+static char __pyx_k_45[] = "the file header.\n \n .. note::\n The header is returned as an iterator over lines without the\n newline character.\n ";
+static char __pyx_k_46[] = "chromosome names";
static char __pyx_k__r[] = "r";
static char __pyx_k__w[] = "w";
static char __pyx_k__bc[] = "bc";
static char __pyx_k__asGTF[] = "asGTF";
static char __pyx_k__asVCF[] = "asVCF";
static char __pyx_k__close[] = "close";
-static char __pyx_k__fetch[] = "fetch";
static char __pyx_k__force[] = "force";
static char __pyx_k__start[] = "start";
static char __pyx_k__types[] = "types";
+static char __pyx_k__append[] = "append";
static char __pyx_k__buffer[] = "buffer";
+static char __pyx_k__ctabix[] = "ctabix";
static char __pyx_k__ctypes[] = "ctypes";
static char __pyx_k__exists[] = "exists";
-static char __pyx_k__header[] = "header";
static char __pyx_k__parser[] = "parser";
static char __pyx_k__pileup[] = "pileup";
static char __pyx_k__preset[] = "preset";
static char __pyx_k__IOError[] = "IOError";
static char __pyx_k__OSError[] = "OSError";
static char __pyx_k____all__[] = "__all__";
-static char __pyx_k____get__[] = "__get__";
static char __pyx_k___isOpen[] = "_isOpen";
static char __pyx_k__asTuple[] = "asTuple";
static char __pyx_k__end_col[] = "end_col";
static char __pyx_k__KeyError[] = "KeyError";
static char __pyx_k__O_RDONLY[] = "O_RDONLY";
static char __pyx_k____main__[] = "__main__";
-static char __pyx_k____next__[] = "__next__";
static char __pyx_k____test__[] = "__test__";
static char __pyx_k__endswith[] = "endswith";
static char __pyx_k__filename[] = "filename";
static char __pyx_k__iterator[] = "iterator";
static char __pyx_k__tempfile[] = "tempfile";
static char __pyx_k__Tabixfile[] = "Tabixfile";
+static char __pyx_k___filename[] = "_filename";
static char __pyx_k__itertools[] = "itertools";
static char __pyx_k__line_skip[] = "line_skip";
static char __pyx_k__meta_char[] = "meta_char";
static char __pyx_k___parseRegion[] = "_parseRegion";
static char __pyx_k__filename_out[] = "filename_out";
static char __pyx_k__StopIteration[] = "StopIteration";
-static char __pyx_k__TabixIterator[] = "TabixIterator";
static char __pyx_k__tabix_compress[] = "tabix_compress";
-static char __pyx_k__TabixHeaderIterator[] = "TabixHeaderIterator";
-static char __pyx_k__TabixIteratorParsed[] = "TabixIteratorParsed";
static PyObject *__pyx_kp_s_1;
static PyObject *__pyx_kp_s_10;
static PyObject *__pyx_kp_s_11;
-static PyObject *__pyx_kp_s_12;
-static PyObject *__pyx_kp_s_13;
-static PyObject *__pyx_kp_s_15;
+static PyObject *__pyx_kp_s_14;
static PyObject *__pyx_kp_s_16;
-static PyObject *__pyx_kp_s_17;
-static PyObject *__pyx_kp_s_18;
static PyObject *__pyx_kp_s_2;
static PyObject *__pyx_kp_s_20;
-static PyObject *__pyx_kp_s_22;
+static PyObject *__pyx_kp_s_21;
static PyObject *__pyx_kp_s_23;
-static PyObject *__pyx_kp_s_24;
static PyObject *__pyx_kp_s_25;
-static PyObject *__pyx_kp_s_26;
-static PyObject *__pyx_kp_u_28;
-static PyObject *__pyx_kp_u_29;
+static PyObject *__pyx_kp_s_29;
static PyObject *__pyx_kp_s_3;
-static PyObject *__pyx_kp_u_30;
-static PyObject *__pyx_kp_u_31;
-static PyObject *__pyx_kp_u_32;
-static PyObject *__pyx_kp_u_33;
-static PyObject *__pyx_kp_u_34;
-static PyObject *__pyx_kp_u_35;
-static PyObject *__pyx_kp_u_36;
-static PyObject *__pyx_kp_u_37;
+static PyObject *__pyx_kp_s_31;
+static PyObject *__pyx_kp_s_32;
+static PyObject *__pyx_kp_s_34;
static PyObject *__pyx_kp_s_4;
+static PyObject *__pyx_kp_s_42;
+static PyObject *__pyx_kp_s_43;
static PyObject *__pyx_kp_s_5;
static PyObject *__pyx_kp_s_6;
static PyObject *__pyx_kp_s_7;
static PyObject *__pyx_n_s__OSError;
static PyObject *__pyx_n_s__O_RDONLY;
static PyObject *__pyx_n_s__StopIteration;
-static PyObject *__pyx_n_s__TabixHeaderIterator;
-static PyObject *__pyx_n_s__TabixIterator;
-static PyObject *__pyx_n_s__TabixIteratorParsed;
static PyObject *__pyx_n_s__Tabixfile;
static PyObject *__pyx_n_s__ValueError;
static PyObject *__pyx_n_s____all__;
-static PyObject *__pyx_n_s____get__;
static PyObject *__pyx_n_s____main__;
-static PyObject *__pyx_n_s____next__;
static PyObject *__pyx_n_s____test__;
+static PyObject *__pyx_n_s___filename;
static PyObject *__pyx_n_s___isOpen;
static PyObject *__pyx_n_s___open;
static PyObject *__pyx_n_s___parseRegion;
+static PyObject *__pyx_n_s__append;
static PyObject *__pyx_n_s__asBed;
static PyObject *__pyx_n_s__asGTF;
static PyObject *__pyx_n_s__asTuple;
static PyObject *__pyx_n_s__buffer;
static PyObject *__pyx_n_s__close;
static PyObject *__pyx_n_s__copy;
+static PyObject *__pyx_n_s__ctabix;
static PyObject *__pyx_n_s__ctypes;
static PyObject *__pyx_n_s__ec;
static PyObject *__pyx_n_s__end;
static PyObject *__pyx_n_s__end_col;
static PyObject *__pyx_n_s__endswith;
static PyObject *__pyx_n_s__exists;
-static PyObject *__pyx_n_s__fetch;
static PyObject *__pyx_n_s__filename;
static PyObject *__pyx_n_s__filename_in;
static PyObject *__pyx_n_s__filename_out;
static PyObject *__pyx_n_s__fp;
static PyObject *__pyx_n_s__gff;
static PyObject *__pyx_n_s__gzip;
-static PyObject *__pyx_n_s__header;
static PyObject *__pyx_n_s__idx;
static PyObject *__pyx_n_s__iterator;
static PyObject *__pyx_n_s__itertools;
static PyObject *__pyx_int_15;
static PyObject *__pyx_int_17;
static PyObject *__pyx_int_18;
-static PyObject *__pyx_int_0x10000;
-static PyObject *__pyx_k_14;
+static PyObject *__pyx_int_65536;
static PyObject *__pyx_k_19;
-static PyObject *__pyx_k_21;
-
-/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":15
+static PyObject *__pyx_k_28;
+static PyObject *__pyx_k_30;
+static PyObject *__pyx_k_tuple_12;
+static PyObject *__pyx_k_tuple_13;
+static PyObject *__pyx_k_tuple_15;
+static PyObject *__pyx_k_tuple_17;
+static PyObject *__pyx_k_tuple_18;
+static PyObject *__pyx_k_tuple_22;
+static PyObject *__pyx_k_tuple_24;
+static PyObject *__pyx_k_tuple_26;
+static PyObject *__pyx_k_tuple_27;
+static PyObject *__pyx_k_tuple_33;
+static PyObject *__pyx_k_tuple_35;
+static PyObject *__pyx_k_tuple_36;
+static PyObject *__pyx_k_tuple_37;
+static PyObject *__pyx_k_tuple_38;
+static PyObject *__pyx_k_tuple_39;
+static PyObject *__pyx_k_tuple_40;
+static PyObject *__pyx_k_tuple_41;
+
+/* "ctabix.pyx":15
* '''
*
* def __cinit__(self, *args, **kwargs ): # <<<<<<<<<<<<<<
__Pyx_INCREF(__pyx_args);
__pyx_v_args = __pyx_args;
- /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":16
+ /* "ctabix.pyx":16
*
* def __cinit__(self, *args, **kwargs ):
* self.tabixfile = NULL # <<<<<<<<<<<<<<
*/
((struct __pyx_obj_6ctabix_Tabixfile *)__pyx_v_self)->tabixfile = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":17
+ /* "ctabix.pyx":17
* def __cinit__(self, *args, **kwargs ):
* self.tabixfile = NULL
* self._open( *args, **kwargs ) # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":19
+/* "ctabix.pyx":19
* self._open( *args, **kwargs )
*
* def _isOpen( self ): # <<<<<<<<<<<<<<
* return self.tabixfile != NULL
*/
-static PyObject *__pyx_pf_6ctabix_9Tabixfile__isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_6ctabix_9Tabixfile__isOpen[] = "Tabixfile._isOpen(self)\nreturn true if samfile has been opened.";
-static PyObject *__pyx_pf_6ctabix_9Tabixfile__isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_6ctabix_9Tabixfile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_6ctabix_9Tabixfile_1_isOpen[] = "Tabixfile._isOpen(self)\nreturn true if samfile has been opened.";
+static PyObject *__pyx_pf_6ctabix_9Tabixfile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
PyObject *__pyx_t_1 = NULL;
__Pyx_RefNannySetupContext("_isOpen");
- /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":21
+ /* "ctabix.pyx":21
* def _isOpen( self ):
* '''return true if samfile has been opened.'''
* return self.tabixfile != NULL # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":23
+/* "ctabix.pyx":23
* return self.tabixfile != NULL
*
* def _open( self, # <<<<<<<<<<<<<<
* mode ='r',
*/
-static PyObject *__pyx_pf_6ctabix_9Tabixfile__open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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-static PyObject *__pyx_pf_6ctabix_9Tabixfile__open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_6ctabix_9Tabixfile_2_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_6ctabix_9Tabixfile_2_open[] = "Tabixfile._open(self, char *filename, mode='r')\nopen a :term:`tabix file` for reading.\n ";
+static PyObject *__pyx_pf_6ctabix_9Tabixfile_2_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
char *__pyx_v_filename;
PyObject *__pyx_v_mode = 0;
PyObject *__pyx_v_filename_index;
__pyx_L4_argument_unpacking_done:;
__pyx_v_filename_index = Py_None; __Pyx_INCREF(Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":30
+ /* "ctabix.pyx":30
* '''
*
* assert mode in ( "r",), "invalid file opening mode `%s`" % mode # <<<<<<<<<<<<<<
*
* # close a previously opened file
*/
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__Pyx_INCREF(__pyx_v_mode);
__pyx_t_1 = __pyx_v_mode;
__pyx_t_2 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":33
+ /* "ctabix.pyx":33
*
* # close a previously opened file
* if self.tabixfile != NULL: self.close() # <<<<<<<<<<<<<<
}
__pyx_L6:;
- /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":34
+ /* "ctabix.pyx":34
* # close a previously opened file
* if self.tabixfile != NULL: self.close()
* self.tabixfile = NULL # <<<<<<<<<<<<<<
*
- * self.filename = filename
+ * if self._filename != NULL: free(self._filename )
*/
((struct __pyx_obj_6ctabix_Tabixfile *)__pyx_v_self)->tabixfile = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":36
+ /* "ctabix.pyx":36
* self.tabixfile = NULL
*
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+ */
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+ * self._filename = strdup( filename ) # <<<<<<<<<<<<<<
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+ * filename_index = filename + ".tbi"
*/
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- /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":37
+ /* "ctabix.pyx":39
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*
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* filename_index = filename + ".tbi" # <<<<<<<<<<<<<<
*
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*/
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__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_v_filename_index);
__pyx_v_filename_index = __pyx_t_1;
__pyx_t_1 = 0;
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+ /* "ctabix.pyx":41
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*
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__Pyx_GOTREF(__pyx_t_1);
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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- /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":43
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- __pyx_t_3 = __Pyx_GetAttrString(__pyx_t_2, "__doc__"); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_34), __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_m, __pyx_n_s__TabixIteratorParsed); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____next__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_GetAttrString(__pyx_t_2, "__doc__"); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_35), __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_m, __pyx_n_s__tabix_compress); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = __Pyx_GetAttrString(__pyx_t_3, "__doc__"); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_36), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_m, __pyx_n_s__tabix_index); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = __Pyx_GetAttrString(__pyx_t_2, "__doc__"); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_37), __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "/ifs/apps/apps/python-2.7.1/lib/python2.7/site-packages/Cython-0.13-py2.7-linux-x86_64.egg/Cython/Includes/cpython/type.pxd":2
+ /* "cpython/type.pxd":2
*
* cdef extern from "Python.h": # <<<<<<<<<<<<<<
* # The C structure of the objects used to describe built-in types.
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
if (__pyx_m) {
__Pyx_AddTraceback("init ctabix");
Py_DECREF(__pyx_m); __pyx_m = 0;
#endif
}
+static int __Pyx_ParseOptionalKeywords(
+ PyObject *kwds,
+ PyObject **argnames[],
+ PyObject *kwds2,
+ PyObject *values[],
+ Py_ssize_t num_pos_args,
+ const char* function_name)
+{
+ PyObject *key = 0, *value = 0;
+ Py_ssize_t pos = 0;
+ PyObject*** name;
+ PyObject*** first_kw_arg = argnames + num_pos_args;
+
+ while (PyDict_Next(kwds, &pos, &key, &value)) {
+ name = first_kw_arg;
+ while (*name && (**name != key)) name++;
+ if (*name) {
+ values[name-argnames] = value;
+ } else {
+ #if PY_MAJOR_VERSION < 3
+ if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
+ #else
+ if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
+ #endif
+ goto invalid_keyword_type;
+ } else {
+ for (name = first_kw_arg; *name; name++) {
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) break;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) break;
+ #endif
+ }
+ if (*name) {
+ values[name-argnames] = value;
+ } else {
+ /* unexpected keyword found */
+ for (name=argnames; name != first_kw_arg; name++) {
+ if (**name == key) goto arg_passed_twice;
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) goto arg_passed_twice;
+ #endif
+ }
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
+ }
+ }
+ }
+ }
+ }
+ return 0;
+arg_passed_twice:
+ __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+ goto bad;
+invalid_keyword_type:
+ PyErr_Format(PyExc_TypeError,
+ "%s() keywords must be strings", function_name);
+ goto bad;
+invalid_keyword:
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION < 3
+ "%s() got an unexpected keyword argument '%s'",
+ function_name, PyString_AsString(key));
+ #else
+ "%s() got an unexpected keyword argument '%U'",
+ function_name, key);
+ #endif
+bad:
+ return -1;
+}
+
static void __Pyx_RaiseArgtupleInvalid(
const char* func_name,
int exact,
num_expected = num_max;
more_or_less = "at most";
}
- if (exact) {
- more_or_less = "exactly";
+ if (exact) {
+ more_or_less = "exactly";
+ }
+ number = (num_expected == 1) ? "" : "s";
+ PyErr_Format(PyExc_TypeError,
+ #if PY_VERSION_HEX < 0x02050000
+ "%s() takes %s %d positional argument%s (%d given)",
+ #else
+ "%s() takes %s %zd positional argument%s (%zd given)",
+ #endif
+ func_name, more_or_less, num_expected, number, num_found);
+}
+
+
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+
+ tmp_type = tstate->curexc_type;
+ tmp_value = tstate->curexc_value;
+ tmp_tb = tstate->curexc_traceback;
+ tstate->curexc_type = type;
+ tstate->curexc_value = value;
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->curexc_type;
+ *value = tstate->curexc_value;
+ *tb = tstate->curexc_traceback;
+
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+}
+
+
+#if PY_MAJOR_VERSION < 3
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ Py_XINCREF(type);
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ /* First, check the traceback argument, replacing None with NULL. */
+ if (tb == Py_None) {
+ Py_DECREF(tb);
+ tb = 0;
+ }
+ else if (tb != NULL && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ /* Next, replace a missing value with None */
+ if (value == NULL) {
+ value = Py_None;
+ Py_INCREF(value);
+ }
+ #if PY_VERSION_HEX < 0x02050000
+ if (!PyClass_Check(type))
+ #else
+ if (!PyType_Check(type))
+ #endif
+ {
+ /* Raising an instance. The value should be a dummy. */
+ if (value != Py_None) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ /* Normalize to raise <class>, <instance> */
+ Py_DECREF(value);
+ value = type;
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+ Py_INCREF(type);
+ }
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
+ #else
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ #endif
+ }
+
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+
+#else /* Python 3+ */
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ if (tb == Py_None) {
+ tb = 0;
+ } else if (tb && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto bad;
+ }
+ if (value == Py_None)
+ value = 0;
+
+ if (PyExceptionInstance_Check(type)) {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto bad;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(value);
+ } else if (!PyExceptionClass_Check(type)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto bad;
}
- number = (num_expected == 1) ? "" : "s";
- PyErr_Format(PyExc_TypeError,
- #if PY_VERSION_HEX < 0x02050000
- "%s() takes %s %d positional argument%s (%d given)",
- #else
- "%s() takes %s %zd positional argument%s (%zd given)",
- #endif
- func_name, more_or_less, num_expected, number, num_found);
-}
-static int __Pyx_ParseOptionalKeywords(
- PyObject *kwds,
- PyObject **argnames[],
- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
- PyObject *key = 0, *value = 0;
- Py_ssize_t pos = 0;
- PyObject*** name;
- PyObject*** first_kw_arg = argnames + num_pos_args;
+ PyErr_SetObject(type, value);
- while (PyDict_Next(kwds, &pos, &key, &value)) {
- name = first_kw_arg;
- while (*name && (**name != key)) name++;
- if (*name) {
- values[name-argnames] = value;
- } else {
- #if PY_MAJOR_VERSION < 3
- if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
- #else
- if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
- #endif
- goto invalid_keyword_type;
- } else {
- for (name = first_kw_arg; *name; name++) {
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) break;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) break;
- #endif
- }
- if (*name) {
- values[name-argnames] = value;
- } else {
- /* unexpected keyword found */
- for (name=argnames; name != first_kw_arg; name++) {
- if (**name == key) goto arg_passed_twice;
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) goto arg_passed_twice;
- #endif
- }
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
- }
- }
- }
+ if (tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* tmp_tb = tstate->curexc_traceback;
+ if (tb != tmp_tb) {
+ Py_INCREF(tb);
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_tb);
}
}
- return 0;
-arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, **name);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%s() got an unexpected keyword argument '%s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
+
bad:
- return -1;
+ return;
}
-
+#endif
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
return module;
}
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
-
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-}
-
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
-
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-}
-
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- /* First, check the traceback argument, replacing None with NULL. */
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- /* Next, replace a missing value with None */
- if (value == NULL) {
- value = Py_None;
- Py_INCREF(value);
- }
- #if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
- #else
- if (!PyType_Check(type))
- #endif
- {
- /* Raising an instance. The value should be a dummy. */
- if (value != Py_None) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- /* Normalize to raise <class>, <instance> */
- Py_DECREF(value);
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
-
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-
-#else /* Python 3+ */
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
-
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
-
- PyErr_SetObject(type, value);
-
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-
-bad:
- return;
-}
-#endif
-
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0;
const int is_unsigned = const_zero < neg_one;
if (!result)
goto bad;
if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
+ PyErr_Format(PyExc_TypeError,
"%s.%s is not a type object",
module_name, class_name);
goto bad;
}
if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
+ PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
#if PY_VERSION_HEX < 0x02050000
#endif
}
else if (((PyTypeObject *)result)->tp_basicsize != size) {
- PyErr_Format(PyExc_ValueError,
+ PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
goto bad;
}
#endif
-static int __Pyx_GetVtable(PyObject *dict, void *vtabptr) {
+static void* __Pyx_GetVtable(PyObject *dict) {
+ void* ptr;
PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
if (!ob)
goto bad;
#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- *(void **)vtabptr = PyCapsule_GetPointer(ob, 0);
+ ptr = PyCapsule_GetPointer(ob, 0);
#else
- *(void **)vtabptr = PyCObject_AsVoidPtr(ob);
+ ptr = PyCObject_AsVoidPtr(ob);
#endif
- if (!*(void **)vtabptr)
- goto bad;
+ if (!ptr && !PyErr_Occurred())
+ PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
Py_DECREF(ob);
- return 0;
+ return ptr;
bad:
Py_XDECREF(ob);
- return -1;
+ return NULL;
}
#include "compile.h"
# char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
cdef class Tabixfile:
- cdef char * filename
+ cdef char * _filename
# pointer to tabixfile
cdef tabix_t * tabixfile
if self.tabixfile != NULL: self.close()
self.tabixfile = NULL
- self.filename = filename
+ if self._filename != NULL: free(self._filename )
+ self._filename = strdup( filename )
+
filename_index = filename + ".tbi"
if mode[0] == 'w':
elif mode[0] == "r":
# open file for reading
- if not os.path.exists( self.filename ):
- raise IOError( "file `%s` not found" % self.filename)
+ if not os.path.exists( self._filename ):
+ raise IOError( "file `%s` not found" % self._filename)
if not os.path.exists( filename_index ):
raise IOError( "index `%s` not found" % filename_index)
# open file and load index
- self.tabixfile = ti_open( self.filename, filename_index )
+ self.tabixfile = ti_open( self._filename, filename_index )
if self.tabixfile == NULL:
raise IOError("could not open file `%s`" % filename )
else:
return TabixIteratorParsed( self, -1, 0, 0, parser )
+ ###############################################################
+ ###############################################################
+ ###############################################################
+ ## properties
+ ###############################################################
+ property filename:
+ '''filename associated with this object.'''
+ def __get__(self):
+ if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ return self._filename
+
property header:
+ '''the file header.
+
+ .. note::
+ The header is returned as an iterator over lines without the
+ newline character.
+ '''
+
def __get__( self ):
- '''return header lines as an iterator.
-
- Note that the header lines do not contain the newline '\n' character.
- '''
return TabixHeaderIterator( self )
property contigs:
result.append( sequences[x] )
return result
+ def close( self ):
+ '''
+ closes the :class:`pysam.Tabixfile`.'''
+ if self.tabixfile != NULL:
+ ti_close( self.tabixfile )
+ self.tabixfile = NULL
+
+ def __dealloc__( self ):
+ # remember: dealloc cannot call other python methods
+ # note: no doc string
+ # note: __del__ is not called.
+ if self.tabixfile != NULL:
+ ti_close( self.tabixfile )
+ self.tabixfile = NULL
+ if self._filename != NULL: free( self._filename )
+
cdef class TabixIterator:
"""iterates over rows in *tabixfile* in region
given by *tid*, *start* and *end*.
pass
cdef class asTuple(Parser):
- '''converts a :term:`tabix row` into a python tuple.'''
+ '''converts a :term:`tabix row` into a python tuple.
+
+ Access is by numeric index.
+ '''
def __call__(self, char * buffer, int len):
cdef TabProxies.TupleProxy r
r = TabProxies.TupleProxy()
return r
cdef class asGTF(Parser):
- '''converts a :term:`tabix row` into a GTF record.'''
+ '''converts a :term:`tabix row` into a GTF record with the following
+ fields:
+
+ contig
+ contig
+ feature
+ feature
+ source
+ source
+ start
+ genomic start coordinate (0-based)
+ end
+ genomic end coordinate plus one (0-based)
+ score
+ feature score
+ strand
+ strand
+ frame
+ frame
+ attributes
+ attribute string.
+
+ GTF formatted entries also defined the attributes:
+
+ gene_id
+ the gene identifier
+ transcript_ind
+ the transcript identifier
+
+ '''
def __call__(self, char * buffer, int len):
cdef TabProxies.GTFProxy r
r = TabProxies.GTFProxy()
return r
cdef class asBed( Parser ):
- '''converts a :term:`tabix row` into a GTF record.'''
+ '''converts a :term:`tabix row` into a bed record
+ with the following fields:
+
+ contig
+ contig
+ start
+ genomic start coordinate (zero-based)
+ end
+ genomic end coordinate plus one (zero-based)
+ name
+ name of feature.
+ score
+ score of feature
+ strand
+ strand of feature
+ thickStart
+ thickStart
+ thickEnd
+ thickEnd
+ itemRGB
+ itemRGB
+ blockCount
+ number of bocks
+ blockSizes
+ ',' separated string of block sizes
+ blockStarts
+ ',' separated string of block genomic start positions
+
+ Only the first three fields are required. Additional
+ fields are optional, but if one is defined, all the preceeding
+ need to be defined as well.
+
+ '''
def __call__(self, char * buffer, int len):
cdef TabProxies.BedProxy r
r = TabProxies.BedProxy()
return r
cdef class asVCF( Parser ):
- '''converts a :term:`tabix row` into a VCF record.'''
+ '''converts a :term:`tabix row` into a VCF record with
+ the following fields:
+
+ contig
+ contig
+ pos
+ chromosomal position, zero-based
+ id
+ id
+ ref
+ reference
+ alt
+ alt
+ qual
+ qual
+ filter
+ filter
+ info
+ info
+ format
+ format specifier.
+
+ Access to genotypes is via index::
+
+ contig = vcf.contig
+ first_sample_genotype = vcf[0]
+ second_sample_genotype = vcf[1]
+
+ '''
def __call__(self, char * buffer, int len ):
cdef TabProxies.VCFProxy r
r = TabProxies.VCFProxy()
-/* Generated by Cython 0.13 on Thu May 5 15:40:49 2011 */
+/* Generated by Cython 0.14.1 on Sat Oct 15 05:27:48 2011 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#define PyBytes_Repr PyString_Repr
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
+#endif
+
+#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#endif
-
#ifndef PySet_CheckExact
-# define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
+ #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
+#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+
#if PY_MAJOR_VERSION >= 3
+ #define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
#define PyInt_Check(op) PyLong_Check(op)
#define PyInt_CheckExact(op) PyLong_CheckExact(op)
#endif
#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
+ #define PyBoolObject PyLongObject
#endif
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
#endif
+#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
+ #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
+ #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
+#else
+ #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
+ #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
+#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
#include "bgzf.h"
#include "tabix.h"
+#ifdef PYREX_WITHOUT_ASSERTIONS
+#define CYTHON_WITHOUT_ASSERTIONS
+#endif
+
+
/* inline attribute */
#ifndef CYTHON_INLINE
#if defined(__GNUC__)
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
#define CYTHON_INLINE inline
#else
- #define CYTHON_INLINE
+ #define CYTHON_INLINE
#endif
#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
# endif
# elif defined(__ICC) || defined(__INTEL_COMPILER)
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
-# define CYTHON_UNUSED
+# define CYTHON_UNUSED
# endif
#endif
#ifdef __GNUC__
/* Test for GCC > 2.95 */
-#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
+#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
#define likely(x) __builtin_expect(!!(x), 1)
#define unlikely(x) __builtin_expect(!!(x), 0)
#else /* __GNUC__ > 2 ... */
/* Type declarations */
-/* "pysam/TabProxies.pxd":42
+/* "TabProxies.pxd":42
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
int is_modified;
};
-/* "pysam/TabProxies.pxd":77
+/* "TabProxies.pxd":77
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
};
-/* "pysam/TabProxies.pxd":80
+/* "TabProxies.pxd":80
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
int bedfields;
};
-/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94
+/* "cvcf.pyx":94
* ###########################################################################################################
*
* cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
uint32_t pos;
};
-/* "pysam/TabProxies.pxd":91
+/* "TabProxies.pxd":91
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
uint32_t pos;
};
-/* "pysam/ctabix.pxd":178
+/* "ctabix.pxd":178
* cdef tabix_t * tabixfile
*
* cdef class Parser: # <<<<<<<<<<<<<<
PyObject_HEAD
};
-/* "pysam/TabProxies.pxd":60
+/* "TabProxies.pxd":60
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
int hasOwnAttributes;
};
-/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":221
+/* "cvcf.pyx":221
*
*
* cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<<
PyObject *vcffile;
};
-/* "pysam/ctabix.pxd":172
+/* "ctabix.pxd":172
* # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
*
* cdef class Tabixfile: # <<<<<<<<<<<<<<
};
-/* "pysam/TabProxies.pxd":42
+/* "TabProxies.pxd":42
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
-/* "pysam/TabProxies.pxd":77
+/* "TabProxies.pxd":77
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
-/* "pysam/TabProxies.pxd":91
+/* "TabProxies.pxd":91
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
-/* "pysam/TabProxies.pxd":60
+/* "TabProxies.pxd":60
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
-/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94
+/* "cvcf.pyx":94
* ###########################################################################################################
*
* cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord;
-/* "pysam/TabProxies.pxd":80
+/* "TabProxies.pxd":80
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name, PyObject* kw_name); /*proto*/
-
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name, PyObject* kw_name); /*proto*/
+
static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+
static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
#define __Pyx_PyObject_AsDouble(obj) \
static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
-
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
-static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, const char *modname); /*proto*/
+static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
+ PyObject *modname); /*proto*/
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+#define __pyx_binding_PyCFunctionType_USED 1
+
+typedef struct {
+ PyCFunctionObject func;
+} __pyx_binding_PyCFunctionType_object;
+
+static PyTypeObject __pyx_binding_PyCFunctionType_type;
+static PyTypeObject *__pyx_binding_PyCFunctionType = NULL;
+
+static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module); /* proto */
+#define __pyx_binding_PyCFunctionType_New(ml, self) __pyx_binding_PyCFunctionType_NewEx(ml, self, NULL)
+
+static int __pyx_binding_PyCFunctionType_init(void); /* proto */
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-static int __Pyx_GetVtable(PyObject *dict, void *vtabptr); /*proto*/
+static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
static PyTypeObject *__pyx_ptype_4cvcf_VCFRecord = 0;
static PyTypeObject *__pyx_ptype_4cvcf_asVCFRecord = 0;
#define __Pyx_MODULE_NAME "cvcf"
-int __pyx_module_is_main_cvcf = 0;
+static int __pyx_module_is_main_cvcf = 0;
/* Implementation of cvcf */
static PyObject *__pyx_builtin_object;
static PyObject *__pyx_builtin_NotImplementedError;
static char __pyx_k_1[] = "";
static char __pyx_k_2[] = ",";
-static char __pyx_k_3[] = ":";
-static char __pyx_k_4[] = "-";
-static char __pyx_k_5[] = "Don't understand region string '%s'";
-static char __pyx_k_6[] = ".";
-static char __pyx_k_7[] = ";";
-static char __pyx_k_8[] = "=";
-static char __pyx_k_9[] = "BAD_NUMBER_OF_VALUES";
-static char __pyx_k_10[] = "(found %s values in element %s; expected %s)";
-static char __pyx_k_11[] = "BAD_NUMBER_OF_PARAMETERS";
-static char __pyx_k_12[] = "id=%s, expected %s parameters, got %s";
-static char __pyx_k_14[] = "Line %s: '%s'\n%s %s: %s\n";
-static char __pyx_k_16[] = "<";
-static char __pyx_k_17[] = "V40_MISSING_ANGLE_BRACKETS";
-static char __pyx_k_18[] = ">";
-static char __pyx_k_19[] = "\"";
-static char __pyx_k_20[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS";
-static char __pyx_k_21[] = "BADLY_FORMATTED_FORMAT_STRING";
-static char __pyx_k_22[] = "ID=";
-static char __pyx_k_23[] = "Number=";
-static char __pyx_k_24[] = "Type=";
-static char __pyx_k_25[] = "Description=";
-static char __pyx_k_26[] = "FORMAT_MISSING_QUOTES";
-static char __pyx_k_27[] = "<none>";
-static char __pyx_k_28[] = "#alleles";
-static char __pyx_k_29[] = "#nonref_alleles";
-static char __pyx_k_30[] = "#genotypes";
-static char __pyx_k_31[] = "#phased_genotypes";
-static char __pyx_k_33[] = "Unknown number type encountered: %s";
-static char __pyx_k_34[] = "%s=%s";
-static char __pyx_k_35[] = "(Undefined tag)";
-static char __pyx_k_38[] = "(output)";
-static char __pyx_k_39[] = "Genotype Quality";
-static char __pyx_k_40[] = "Read depth at this position for this sample";
-static char __pyx_k_41[] = "Haplotype Quality";
-static char __pyx_k_42[] = "Sample Genotype Filter";
-static char __pyx_k_43[] = "##";
-static char __pyx_k_44[] = "VCFv3.3";
-static char __pyx_k_45[] = "VCFv4.0";
-static char __pyx_k_46[] = "VCFv4.1";
-static char __pyx_k_47[] = "UNKNOWN_FORMAT_STRING";
-static char __pyx_k_48[] = "##fileformat=VCFv%s.%s\n";
-static char __pyx_k_49[] = "##%s=%s\n";
-static char __pyx_k_50[] = "#";
-static char __pyx_k_51[] = "\t";
-static char __pyx_k_52[] = "HEADING_NOT_SEPARATED_BY_TABS";
-static char __pyx_k_53[] = "(%sth entry not found)";
-static char __pyx_k_54[] = "(found %s, expected %s)";
-static char __pyx_k_55[] = "BADLY_FORMATTED_HEADING";
-static char __pyx_k_56[] = "\n";
-static char __pyx_k_57[] = "|";
-static char __pyx_k_58[] = "ERROR_FLAG_HAS_VALUE";
-static char __pyx_k_59[] = "ERROR_FORMAT_NOT_NUMERICAL";
-static char __pyx_k_60[] = "ERROR_FORMAT_NOT_CHAR";
-static char __pyx_k_62[] = "BAD_NUMBER_OF_COLUMNS";
-static char __pyx_k_63[] = "expected %s for %s samples (%s), got %s";
-static char __pyx_k_64[] = "(reference is %s, VCF says %s)";
-static char __pyx_k_65[] = "V33_UNMATCHED_DELETION";
-static char __pyx_k_66[] = "(deletion is %s, reference is %s)";
-static char __pyx_k_67[] = "MISSING_INDEL_ALLELE_REF_BASE";
-static char __pyx_k_68[] = "Required key %s not found in data";
-static char __pyx_k_69[] = "enter_default_format";
-static char __pyx_k_70[] = "Can only handle v3.3 and v4.0 VCF files";
-static char __pyx_k_71[] = "Invalid error string: %s";
-static char __pyx_k_72[] = "needs to be checked";
-static char __pyx_k_73[] = "[|/\\\\]";
-static char __pyx_k_74[] = "^[ACGTN]+$";
-static char __pyx_k_75[] = "id numbertype number type description missingvalue";
-static char __pyx_k_76[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
-static char __pyx_k_77[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string";
-static char __pyx_k_78[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s";
-static char __pyx_k_79[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)";
-static char __pyx_k_80[] = "POS_NOT_NUMERICAL:Position column is not numerical";
-static char __pyx_k_81[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field";
-static char __pyx_k_82[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF";
-static char __pyx_k_83[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF";
-static char __pyx_k_84[] = "POS_NOT_POSITIVE:Position field must be >0";
-static char __pyx_k_85[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'";
-static char __pyx_k_86[] = "ERROR_INFO_STRING:Error while parsing info field";
-static char __pyx_k_87[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)";
-static char __pyx_k_88[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s";
-static char __pyx_k_89[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string";
-static char __pyx_k_90[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header";
-static char __pyx_k_91[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header";
-static char __pyx_k_92[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)";
-static char __pyx_k_93[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)";
-static char __pyx_k_94[] = "BAD_GENOTYPE:Cannot parse genotype (%s)";
-static char __pyx_k_95[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)";
-static char __pyx_k_96[] = "MISSING_REF:Reference allele missing";
-static char __pyx_k_97[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)";
-static char __pyx_k_98[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets";
-static char __pyx_k_99[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes";
+static char __pyx_k_4[] = ":";
+static char __pyx_k_6[] = "-";
+static char __pyx_k_8[] = "Don't understand region string '%s'";
+static char __pyx_k_9[] = ".";
+static char __pyx_k_11[] = ";";
+static char __pyx_k_14[] = "=";
+static char __pyx_k_18[] = "BAD_NUMBER_OF_VALUES";
+static char __pyx_k_19[] = "(found %s values in element %s; expected %s)";
+static char __pyx_k_20[] = "BAD_NUMBER_OF_PARAMETERS";
+static char __pyx_k_21[] = "id=%s, expected %s parameters, got %s";
+static char __pyx_k_25[] = "Line %s: '%s'\n%s %s: %s\n";
+static char __pyx_k_27[] = "<";
+static char __pyx_k_29[] = "V40_MISSING_ANGLE_BRACKETS";
+static char __pyx_k_30[] = ">";
+static char __pyx_k_34[] = "\"";
+static char __pyx_k_38[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS";
+static char __pyx_k_39[] = "BADLY_FORMATTED_FORMAT_STRING";
+static char __pyx_k_40[] = "ID=";
+static char __pyx_k_41[] = "Number=";
+static char __pyx_k_42[] = "Type=";
+static char __pyx_k_43[] = "Description=";
+static char __pyx_k_52[] = "FORMAT_MISSING_QUOTES";
+static char __pyx_k_55[] = "<none>";
+static char __pyx_k_56[] = "#alleles";
+static char __pyx_k_57[] = "#nonref_alleles";
+static char __pyx_k_58[] = "#genotypes";
+static char __pyx_k_59[] = "#phased_genotypes";
+static char __pyx_k_61[] = "Unknown number type encountered: %s";
+static char __pyx_k_62[] = "%s=%s";
+static char __pyx_k_63[] = "(Undefined tag)";
+static char __pyx_k_66[] = "(output)";
+static char __pyx_k_69[] = "Genotype Quality";
+static char __pyx_k_70[] = "Read depth at this position for this sample";
+static char __pyx_k_71[] = "Haplotype Quality";
+static char __pyx_k_72[] = "Sample Genotype Filter";
+static char __pyx_k_73[] = "##";
+static char __pyx_k_76[] = "VCFv3.3";
+static char __pyx_k_77[] = "VCFv4.0";
+static char __pyx_k_78[] = "VCFv4.1";
+static char __pyx_k_79[] = "UNKNOWN_FORMAT_STRING";
+static char __pyx_k_80[] = "##fileformat=VCFv%s.%s\n";
+static char __pyx_k_81[] = "##%s=%s\n";
+static char __pyx_k_82[] = "#";
+static char __pyx_k_85[] = "\t";
+static char __pyx_k_87[] = "HEADING_NOT_SEPARATED_BY_TABS";
+static char __pyx_k_88[] = "(%sth entry not found)";
+static char __pyx_k_89[] = "(found %s, expected %s)";
+static char __pyx_k_90[] = "BADLY_FORMATTED_HEADING";
+static char __pyx_k_91[] = "\n";
+static char __pyx_k_92[] = "|";
+static char __pyx_k_93[] = "ERROR_FLAG_HAS_VALUE";
+static char __pyx_k_97[] = "ERROR_FORMAT_NOT_NUMERICAL";
+static char __pyx_k_98[] = "ERROR_FORMAT_NOT_CHAR";
static char __pyx_k__0[] = "0";
static char __pyx_k__D[] = "D";
static char __pyx_k__I[] = "I";
static char __pyx_k__N[] = "N";
-static char __pyx_k_100[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields";
-static char __pyx_k_101[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs";
-static char __pyx_k_102[] = "WRONG_REF:Wrong reference %s";
-static char __pyx_k_103[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data";
-static char __pyx_k_104[] = "BAD_CHR_TAG:Error calculating chr tag for %s";
-static char __pyx_k_105[] = "ZERO_LENGTH_ALLELE:Found zero-length allele";
-static char __pyx_k_106[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base";
-static char __pyx_k_107[] = "VCF.getsamples (line 880)";
-static char __pyx_k_108[] = "VCF.setsamples (line 884)";
-static char __pyx_k_109[] = "VCF.getheader (line 888)";
-static char __pyx_k_110[] = "VCF.setheader (line 892)";
-static char __pyx_k_111[] = "VCF.getinfo (line 896)";
-static char __pyx_k_112[] = "VCF.setinfo (line 900)";
-static char __pyx_k_113[] = "VCF.getformat (line 904)";
-static char __pyx_k_114[] = "VCF.setformat (line 908)";
-static char __pyx_k_115[] = "VCF.getfilter (line 912)";
-static char __pyx_k_116[] = "VCF.setfilter (line 916)";
-static char __pyx_k_117[] = "VCF.setreference (line 927)";
-static char __pyx_k_118[] = "VCF.parse (line 939)";
-static char __pyx_k_119[] = "VCF.write (line 946)";
-static char __pyx_k_120[] = "VCF.writeheader (line 952)";
-static char __pyx_k_121[] = "VCF.compare_calls (line 957)";
-static char __pyx_k_122[] = "VCF.connect (line 979)";
-static char __pyx_k_123[] = "VCF.fetch (line 984)";
-static char __pyx_k_124[] = "VCF.validate (line 993)";
+static char __pyx_k_101[] = "BAD_NUMBER_OF_COLUMNS";
+static char __pyx_k_102[] = "expected %s for %s samples (%s), got %s";
+static char __pyx_k_103[] = "(reference is %s, VCF says %s)";
+static char __pyx_k_111[] = "V33_UNMATCHED_DELETION";
+static char __pyx_k_112[] = "(deletion is %s, reference is %s)";
+static char __pyx_k_113[] = "MISSING_INDEL_ALLELE_REF_BASE";
+static char __pyx_k_115[] = "Required key %s not found in data";
+static char __pyx_k_118[] = "enter_default_format";
+static char __pyx_k_119[] = "Can only handle v3.3 and v4.0 VCF files";
+static char __pyx_k_121[] = "Invalid error string: %s";
+static char __pyx_k_122[] = "needs to be checked";
+static char __pyx_k_126[] = "[|/\\\\]";
+static char __pyx_k_128[] = "^[ACGTN]+$";
+static char __pyx_k_130[] = "id numbertype number type description missingvalue";
+static char __pyx_k_132[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
+static char __pyx_k_133[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string";
+static char __pyx_k_134[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s";
+static char __pyx_k_135[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)";
+static char __pyx_k_136[] = "POS_NOT_NUMERICAL:Position column is not numerical";
+static char __pyx_k_137[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field";
+static char __pyx_k_138[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF";
+static char __pyx_k_139[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF";
+static char __pyx_k_140[] = "POS_NOT_POSITIVE:Position field must be >0";
+static char __pyx_k_141[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'";
+static char __pyx_k_142[] = "ERROR_INFO_STRING:Error while parsing info field";
+static char __pyx_k_143[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)";
+static char __pyx_k_144[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s";
+static char __pyx_k_145[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string";
+static char __pyx_k_146[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header";
+static char __pyx_k_147[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header";
+static char __pyx_k_148[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)";
+static char __pyx_k_149[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)";
+static char __pyx_k_150[] = "BAD_GENOTYPE:Cannot parse genotype (%s)";
+static char __pyx_k_151[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)";
+static char __pyx_k_152[] = "MISSING_REF:Reference allele missing";
+static char __pyx_k_153[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)";
+static char __pyx_k_154[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets";
+static char __pyx_k_155[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes";
+static char __pyx_k_156[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields";
+static char __pyx_k_157[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs";
+static char __pyx_k_158[] = "WRONG_REF:Wrong reference %s";
+static char __pyx_k_159[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data";
+static char __pyx_k_160[] = "BAD_CHR_TAG:Error calculating chr tag for %s";
+static char __pyx_k_161[] = "ZERO_LENGTH_ALLELE:Found zero-length allele";
+static char __pyx_k_162[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base";
static char __pyx_k__DP[] = "DP";
static char __pyx_k__FT[] = "FT";
static char __pyx_k__GQ[] = "GQ";
static char __pyx_k__alt1[] = "alt1";
static char __pyx_k__alt2[] = "alt2";
static char __pyx_k__copy[] = "copy";
+static char __pyx_k__cvcf[] = "cvcf";
static char __pyx_k__data[] = "data";
static char __pyx_k__find[] = "find";
static char __pyx_k__info[] = "info";
static char __pyx_k__String[] = "String";
static char __pyx_k___lines[] = "_lines";
static char __pyx_k___parse[] = "_parse";
+static char __pyx_k__append[] = "append";
static char __pyx_k__bisect[] = "bisect";
static char __pyx_k__buffer[] = "buffer";
static char __pyx_k__contig[] = "contig";
static char __pyx_k__datagenerator[] = "datagenerator";
static char __pyx_k__format_format[] = "format_format";
static char __pyx_k__parse_heading[] = "parse_heading";
+static char __pyx_k__parse_regions[] = "parse_regions";
static char __pyx_k__write_heading[] = "write_heading";
static char __pyx_k__V33_BAD_ALLELE[] = "V33_BAD_ALLELE";
static char __pyx_k__V40_BAD_ALLELE[] = "V40_BAD_ALLELE";
static char __pyx_k__NotImplementedError[] = "NotImplementedError";
static char __pyx_k__UNKNOWN_CHAR_IN_REF[] = "UNKNOWN_CHAR_IN_REF";
static PyObject *__pyx_kp_s_1;
-static PyObject *__pyx_kp_s_10;
-static PyObject *__pyx_kp_s_100;
-static PyObject *__pyx_kp_s_101;
+static PyObject *__pyx_n_s_101;
static PyObject *__pyx_kp_s_102;
static PyObject *__pyx_kp_s_103;
-static PyObject *__pyx_kp_s_104;
-static PyObject *__pyx_kp_s_105;
-static PyObject *__pyx_kp_s_106;
-static PyObject *__pyx_kp_u_107;
-static PyObject *__pyx_kp_u_108;
-static PyObject *__pyx_kp_u_109;
-static PyObject *__pyx_n_s_11;
-static PyObject *__pyx_kp_u_110;
-static PyObject *__pyx_kp_u_111;
-static PyObject *__pyx_kp_u_112;
-static PyObject *__pyx_kp_u_113;
-static PyObject *__pyx_kp_u_114;
-static PyObject *__pyx_kp_u_115;
-static PyObject *__pyx_kp_u_116;
-static PyObject *__pyx_kp_u_117;
-static PyObject *__pyx_kp_u_118;
-static PyObject *__pyx_kp_u_119;
-static PyObject *__pyx_kp_s_12;
-static PyObject *__pyx_kp_u_120;
-static PyObject *__pyx_kp_u_121;
-static PyObject *__pyx_kp_u_122;
-static PyObject *__pyx_kp_u_123;
-static PyObject *__pyx_kp_u_124;
+static PyObject *__pyx_kp_s_11;
+static PyObject *__pyx_n_s_111;
+static PyObject *__pyx_kp_s_112;
+static PyObject *__pyx_n_s_113;
+static PyObject *__pyx_kp_s_115;
+static PyObject *__pyx_n_s_118;
+static PyObject *__pyx_kp_s_119;
+static PyObject *__pyx_kp_s_121;
+static PyObject *__pyx_kp_s_122;
+static PyObject *__pyx_kp_s_126;
+static PyObject *__pyx_kp_s_128;
+static PyObject *__pyx_kp_s_130;
+static PyObject *__pyx_kp_s_132;
+static PyObject *__pyx_kp_s_133;
+static PyObject *__pyx_kp_s_134;
+static PyObject *__pyx_kp_s_135;
+static PyObject *__pyx_kp_s_136;
+static PyObject *__pyx_kp_s_137;
+static PyObject *__pyx_kp_s_138;
+static PyObject *__pyx_kp_s_139;
static PyObject *__pyx_kp_s_14;
-static PyObject *__pyx_kp_s_16;
-static PyObject *__pyx_n_s_17;
-static PyObject *__pyx_kp_s_18;
+static PyObject *__pyx_kp_s_140;
+static PyObject *__pyx_kp_s_141;
+static PyObject *__pyx_kp_s_142;
+static PyObject *__pyx_kp_s_143;
+static PyObject *__pyx_kp_s_144;
+static PyObject *__pyx_kp_s_145;
+static PyObject *__pyx_kp_s_146;
+static PyObject *__pyx_kp_s_147;
+static PyObject *__pyx_kp_s_148;
+static PyObject *__pyx_kp_s_149;
+static PyObject *__pyx_kp_s_150;
+static PyObject *__pyx_kp_s_151;
+static PyObject *__pyx_kp_s_152;
+static PyObject *__pyx_kp_s_153;
+static PyObject *__pyx_kp_s_154;
+static PyObject *__pyx_kp_s_155;
+static PyObject *__pyx_kp_s_156;
+static PyObject *__pyx_kp_s_157;
+static PyObject *__pyx_kp_s_158;
+static PyObject *__pyx_kp_s_159;
+static PyObject *__pyx_kp_s_160;
+static PyObject *__pyx_kp_s_161;
+static PyObject *__pyx_kp_s_162;
+static PyObject *__pyx_n_s_18;
static PyObject *__pyx_kp_s_19;
static PyObject *__pyx_kp_s_2;
static PyObject *__pyx_n_s_20;
-static PyObject *__pyx_n_s_21;
-static PyObject *__pyx_kp_s_22;
-static PyObject *__pyx_kp_s_23;
-static PyObject *__pyx_kp_s_24;
+static PyObject *__pyx_kp_s_21;
static PyObject *__pyx_kp_s_25;
-static PyObject *__pyx_n_s_26;
static PyObject *__pyx_kp_s_27;
-static PyObject *__pyx_kp_s_28;
-static PyObject *__pyx_kp_s_29;
-static PyObject *__pyx_kp_s_3;
+static PyObject *__pyx_n_s_29;
static PyObject *__pyx_kp_s_30;
-static PyObject *__pyx_kp_s_31;
-static PyObject *__pyx_kp_s_33;
static PyObject *__pyx_kp_s_34;
-static PyObject *__pyx_kp_s_35;
-static PyObject *__pyx_kp_s_38;
-static PyObject *__pyx_kp_s_39;
+static PyObject *__pyx_n_s_38;
+static PyObject *__pyx_n_s_39;
static PyObject *__pyx_kp_s_4;
static PyObject *__pyx_kp_s_40;
static PyObject *__pyx_kp_s_41;
static PyObject *__pyx_kp_s_42;
static PyObject *__pyx_kp_s_43;
-static PyObject *__pyx_kp_s_44;
-static PyObject *__pyx_kp_s_45;
-static PyObject *__pyx_kp_s_46;
-static PyObject *__pyx_n_s_47;
-static PyObject *__pyx_kp_s_48;
-static PyObject *__pyx_kp_s_49;
-static PyObject *__pyx_kp_s_5;
-static PyObject *__pyx_kp_s_50;
-static PyObject *__pyx_kp_s_51;
static PyObject *__pyx_n_s_52;
-static PyObject *__pyx_kp_s_53;
-static PyObject *__pyx_kp_s_54;
-static PyObject *__pyx_n_s_55;
+static PyObject *__pyx_kp_s_55;
static PyObject *__pyx_kp_s_56;
static PyObject *__pyx_kp_s_57;
-static PyObject *__pyx_n_s_58;
-static PyObject *__pyx_n_s_59;
-static PyObject *__pyx_kp_b_6;
+static PyObject *__pyx_kp_s_58;
+static PyObject *__pyx_kp_s_59;
static PyObject *__pyx_kp_s_6;
-static PyObject *__pyx_n_s_60;
-static PyObject *__pyx_n_s_62;
+static PyObject *__pyx_kp_s_61;
+static PyObject *__pyx_kp_s_62;
static PyObject *__pyx_kp_s_63;
-static PyObject *__pyx_kp_s_64;
-static PyObject *__pyx_n_s_65;
static PyObject *__pyx_kp_s_66;
-static PyObject *__pyx_n_s_67;
-static PyObject *__pyx_kp_s_68;
-static PyObject *__pyx_n_s_69;
-static PyObject *__pyx_kp_s_7;
+static PyObject *__pyx_kp_s_69;
static PyObject *__pyx_kp_s_70;
static PyObject *__pyx_kp_s_71;
static PyObject *__pyx_kp_s_72;
static PyObject *__pyx_kp_s_73;
-static PyObject *__pyx_kp_s_74;
-static PyObject *__pyx_kp_s_75;
static PyObject *__pyx_kp_s_76;
static PyObject *__pyx_kp_s_77;
static PyObject *__pyx_kp_s_78;
-static PyObject *__pyx_kp_s_79;
+static PyObject *__pyx_n_s_79;
static PyObject *__pyx_kp_s_8;
static PyObject *__pyx_kp_s_80;
static PyObject *__pyx_kp_s_81;
static PyObject *__pyx_kp_s_82;
-static PyObject *__pyx_kp_s_83;
-static PyObject *__pyx_kp_s_84;
static PyObject *__pyx_kp_s_85;
-static PyObject *__pyx_kp_s_86;
-static PyObject *__pyx_kp_s_87;
+static PyObject *__pyx_n_s_87;
static PyObject *__pyx_kp_s_88;
static PyObject *__pyx_kp_s_89;
-static PyObject *__pyx_n_s_9;
-static PyObject *__pyx_kp_s_90;
+static PyObject *__pyx_kp_b_9;
+static PyObject *__pyx_kp_s_9;
+static PyObject *__pyx_n_s_90;
static PyObject *__pyx_kp_s_91;
static PyObject *__pyx_kp_s_92;
-static PyObject *__pyx_kp_s_93;
-static PyObject *__pyx_kp_s_94;
-static PyObject *__pyx_kp_s_95;
-static PyObject *__pyx_kp_s_96;
-static PyObject *__pyx_kp_s_97;
-static PyObject *__pyx_kp_s_98;
-static PyObject *__pyx_kp_s_99;
+static PyObject *__pyx_n_s_93;
+static PyObject *__pyx_n_s_97;
+static PyObject *__pyx_n_s_98;
+static PyObject *__pyx_kp_b__0;
static PyObject *__pyx_kp_s__0;
static PyObject *__pyx_n_s__ACGTN;
static PyObject *__pyx_n_s__ALT;
static PyObject *__pyx_n_s__NT_UNKNOWN;
static PyObject *__pyx_n_s__NotImplementedError;
static PyObject *__pyx_n_s__Number;
+static PyObject *__pyx_n_b__PASS;
static PyObject *__pyx_n_s__PASS;
static PyObject *__pyx_n_s__POS;
static PyObject *__pyx_n_s__POS_NOT_NUMERICAL;
static PyObject *__pyx_n_s__alt;
static PyObject *__pyx_n_s__alt1;
static PyObject *__pyx_n_s__alt2;
+static PyObject *__pyx_n_s__append;
static PyObject *__pyx_n_s__bisect;
static PyObject *__pyx_n_s__buffer;
static PyObject *__pyx_n_s__chrom;
static PyObject *__pyx_n_s__convertGT;
static PyObject *__pyx_n_s__convertGTback;
static PyObject *__pyx_n_s__copy;
+static PyObject *__pyx_n_s__cvcf;
static PyObject *__pyx_n_s__data;
static PyObject *__pyx_n_s__datagenerator;
static PyObject *__pyx_n_s__deepcopy;
static PyObject *__pyx_n_s__parse_formatdata;
static PyObject *__pyx_n_s__parse_header;
static PyObject *__pyx_n_s__parse_heading;
+static PyObject *__pyx_n_s__parse_regions;
static PyObject *__pyx_n_s__parser;
static PyObject *__pyx_n_s__pos;
static PyObject *__pyx_n_s__pos1;
static PyObject *__pyx_int_40;
static PyObject *__pyx_int_100;
static PyObject *__pyx_int_3000000000;
-static PyObject *__pyx_k_13;
-static PyObject *__pyx_k_15;
-static PyObject *__pyx_k_32;
-static PyObject *__pyx_k_36;
-static PyObject *__pyx_k_37;
-static PyObject *__pyx_k_61;
-
-/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":58
+static PyObject *__pyx_k_22;
+static PyObject *__pyx_k_26;
+static PyObject *__pyx_k_60;
+static PyObject *__pyx_k_64;
+static PyObject *__pyx_k_65;
+static PyObject *__pyx_k_99;
+static PyObject *__pyx_k_tuple_3;
+static PyObject *__pyx_k_tuple_5;
+static PyObject *__pyx_k_tuple_7;
+static PyObject *__pyx_k_tuple_10;
+static PyObject *__pyx_k_tuple_12;
+static PyObject *__pyx_k_tuple_13;
+static PyObject *__pyx_k_tuple_15;
+static PyObject *__pyx_k_tuple_16;
+static PyObject *__pyx_k_tuple_17;
+static PyObject *__pyx_k_tuple_23;
+static PyObject *__pyx_k_tuple_24;
+static PyObject *__pyx_k_tuple_28;
+static PyObject *__pyx_k_tuple_31;
+static PyObject *__pyx_k_tuple_32;
+static PyObject *__pyx_k_tuple_33;
+static PyObject *__pyx_k_tuple_35;
+static PyObject *__pyx_k_tuple_36;
+static PyObject *__pyx_k_tuple_37;
+static PyObject *__pyx_k_tuple_44;
+static PyObject *__pyx_k_tuple_45;
+static PyObject *__pyx_k_tuple_46;
+static PyObject *__pyx_k_tuple_47;
+static PyObject *__pyx_k_tuple_48;
+static PyObject *__pyx_k_tuple_49;
+static PyObject *__pyx_k_tuple_50;
+static PyObject *__pyx_k_tuple_51;
+static PyObject *__pyx_k_tuple_53;
+static PyObject *__pyx_k_tuple_54;
+static PyObject *__pyx_k_tuple_67;
+static PyObject *__pyx_k_tuple_68;
+static PyObject *__pyx_k_tuple_74;
+static PyObject *__pyx_k_tuple_75;
+static PyObject *__pyx_k_tuple_83;
+static PyObject *__pyx_k_tuple_84;
+static PyObject *__pyx_k_tuple_86;
+static PyObject *__pyx_k_tuple_94;
+static PyObject *__pyx_k_tuple_95;
+static PyObject *__pyx_k_tuple_96;
+static PyObject *__pyx_k_tuple_100;
+static PyObject *__pyx_k_tuple_104;
+static PyObject *__pyx_k_tuple_105;
+static PyObject *__pyx_k_tuple_106;
+static PyObject *__pyx_k_tuple_107;
+static PyObject *__pyx_k_tuple_108;
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- {&__pyx_kp_s_28, __pyx_k_28, sizeof(__pyx_k_28), 0, 0, 1, 0},
- {&__pyx_kp_s_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 1, 0},
- {&__pyx_kp_s_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 0, 1, 0},
+ {&__pyx_n_s_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 1, 1},
{&__pyx_kp_s_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 0, 1, 0},
- {&__pyx_kp_s_31, __pyx_k_31, sizeof(__pyx_k_31), 0, 0, 1, 0},
- {&__pyx_kp_s_33, __pyx_k_33, sizeof(__pyx_k_33), 0, 0, 1, 0},
{&__pyx_kp_s_34, __pyx_k_34, sizeof(__pyx_k_34), 0, 0, 1, 0},
- {&__pyx_kp_s_35, __pyx_k_35, sizeof(__pyx_k_35), 0, 0, 1, 0},
- {&__pyx_kp_s_38, __pyx_k_38, sizeof(__pyx_k_38), 0, 0, 1, 0},
- {&__pyx_kp_s_39, __pyx_k_39, sizeof(__pyx_k_39), 0, 0, 1, 0},
+ {&__pyx_n_s_38, __pyx_k_38, sizeof(__pyx_k_38), 0, 0, 1, 1},
+ {&__pyx_n_s_39, __pyx_k_39, sizeof(__pyx_k_39), 0, 0, 1, 1},
{&__pyx_kp_s_4, __pyx_k_4, sizeof(__pyx_k_4), 0, 0, 1, 0},
{&__pyx_kp_s_40, __pyx_k_40, sizeof(__pyx_k_40), 0, 0, 1, 0},
{&__pyx_kp_s_41, __pyx_k_41, sizeof(__pyx_k_41), 0, 0, 1, 0},
{&__pyx_kp_s_42, __pyx_k_42, sizeof(__pyx_k_42), 0, 0, 1, 0},
{&__pyx_kp_s_43, __pyx_k_43, sizeof(__pyx_k_43), 0, 0, 1, 0},
- {&__pyx_kp_s_44, __pyx_k_44, sizeof(__pyx_k_44), 0, 0, 1, 0},
- {&__pyx_kp_s_45, __pyx_k_45, sizeof(__pyx_k_45), 0, 0, 1, 0},
- {&__pyx_kp_s_46, __pyx_k_46, sizeof(__pyx_k_46), 0, 0, 1, 0},
- {&__pyx_n_s_47, __pyx_k_47, sizeof(__pyx_k_47), 0, 0, 1, 1},
- {&__pyx_kp_s_48, __pyx_k_48, sizeof(__pyx_k_48), 0, 0, 1, 0},
- {&__pyx_kp_s_49, __pyx_k_49, sizeof(__pyx_k_49), 0, 0, 1, 0},
- {&__pyx_kp_s_5, __pyx_k_5, sizeof(__pyx_k_5), 0, 0, 1, 0},
- {&__pyx_kp_s_50, __pyx_k_50, sizeof(__pyx_k_50), 0, 0, 1, 0},
- {&__pyx_kp_s_51, __pyx_k_51, sizeof(__pyx_k_51), 0, 0, 1, 0},
{&__pyx_n_s_52, __pyx_k_52, sizeof(__pyx_k_52), 0, 0, 1, 1},
- {&__pyx_kp_s_53, __pyx_k_53, sizeof(__pyx_k_53), 0, 0, 1, 0},
- {&__pyx_kp_s_54, __pyx_k_54, sizeof(__pyx_k_54), 0, 0, 1, 0},
- {&__pyx_n_s_55, __pyx_k_55, sizeof(__pyx_k_55), 0, 0, 1, 1},
+ {&__pyx_kp_s_55, __pyx_k_55, sizeof(__pyx_k_55), 0, 0, 1, 0},
{&__pyx_kp_s_56, __pyx_k_56, sizeof(__pyx_k_56), 0, 0, 1, 0},
{&__pyx_kp_s_57, __pyx_k_57, sizeof(__pyx_k_57), 0, 0, 1, 0},
- {&__pyx_n_s_58, __pyx_k_58, sizeof(__pyx_k_58), 0, 0, 1, 1},
- {&__pyx_n_s_59, __pyx_k_59, sizeof(__pyx_k_59), 0, 0, 1, 1},
- {&__pyx_kp_b_6, __pyx_k_6, sizeof(__pyx_k_6), 0, 0, 0, 0},
+ {&__pyx_kp_s_58, __pyx_k_58, sizeof(__pyx_k_58), 0, 0, 1, 0},
+ {&__pyx_kp_s_59, __pyx_k_59, sizeof(__pyx_k_59), 0, 0, 1, 0},
{&__pyx_kp_s_6, __pyx_k_6, sizeof(__pyx_k_6), 0, 0, 1, 0},
- {&__pyx_n_s_60, __pyx_k_60, sizeof(__pyx_k_60), 0, 0, 1, 1},
- {&__pyx_n_s_62, __pyx_k_62, sizeof(__pyx_k_62), 0, 0, 1, 1},
+ {&__pyx_kp_s_61, __pyx_k_61, sizeof(__pyx_k_61), 0, 0, 1, 0},
+ {&__pyx_kp_s_62, __pyx_k_62, sizeof(__pyx_k_62), 0, 0, 1, 0},
{&__pyx_kp_s_63, __pyx_k_63, sizeof(__pyx_k_63), 0, 0, 1, 0},
- {&__pyx_kp_s_64, __pyx_k_64, sizeof(__pyx_k_64), 0, 0, 1, 0},
- {&__pyx_n_s_65, __pyx_k_65, sizeof(__pyx_k_65), 0, 0, 1, 1},
{&__pyx_kp_s_66, __pyx_k_66, sizeof(__pyx_k_66), 0, 0, 1, 0},
- {&__pyx_n_s_67, __pyx_k_67, sizeof(__pyx_k_67), 0, 0, 1, 1},
- {&__pyx_kp_s_68, __pyx_k_68, sizeof(__pyx_k_68), 0, 0, 1, 0},
- {&__pyx_n_s_69, __pyx_k_69, sizeof(__pyx_k_69), 0, 0, 1, 1},
- {&__pyx_kp_s_7, __pyx_k_7, sizeof(__pyx_k_7), 0, 0, 1, 0},
+ {&__pyx_kp_s_69, __pyx_k_69, sizeof(__pyx_k_69), 0, 0, 1, 0},
{&__pyx_kp_s_70, __pyx_k_70, sizeof(__pyx_k_70), 0, 0, 1, 0},
{&__pyx_kp_s_71, __pyx_k_71, sizeof(__pyx_k_71), 0, 0, 1, 0},
{&__pyx_kp_s_72, __pyx_k_72, sizeof(__pyx_k_72), 0, 0, 1, 0},
{&__pyx_kp_s_73, __pyx_k_73, sizeof(__pyx_k_73), 0, 0, 1, 0},
- {&__pyx_kp_s_74, __pyx_k_74, sizeof(__pyx_k_74), 0, 0, 1, 0},
- {&__pyx_kp_s_75, __pyx_k_75, sizeof(__pyx_k_75), 0, 0, 1, 0},
{&__pyx_kp_s_76, __pyx_k_76, sizeof(__pyx_k_76), 0, 0, 1, 0},
{&__pyx_kp_s_77, __pyx_k_77, sizeof(__pyx_k_77), 0, 0, 1, 0},
{&__pyx_kp_s_78, __pyx_k_78, sizeof(__pyx_k_78), 0, 0, 1, 0},
- {&__pyx_kp_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 0},
+ {&__pyx_n_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 1},
{&__pyx_kp_s_8, __pyx_k_8, sizeof(__pyx_k_8), 0, 0, 1, 0},
{&__pyx_kp_s_80, __pyx_k_80, sizeof(__pyx_k_80), 0, 0, 1, 0},
{&__pyx_kp_s_81, __pyx_k_81, sizeof(__pyx_k_81), 0, 0, 1, 0},
{&__pyx_kp_s_82, __pyx_k_82, sizeof(__pyx_k_82), 0, 0, 1, 0},
- {&__pyx_kp_s_83, __pyx_k_83, sizeof(__pyx_k_83), 0, 0, 1, 0},
- {&__pyx_kp_s_84, __pyx_k_84, sizeof(__pyx_k_84), 0, 0, 1, 0},
{&__pyx_kp_s_85, __pyx_k_85, sizeof(__pyx_k_85), 0, 0, 1, 0},
- {&__pyx_kp_s_86, __pyx_k_86, sizeof(__pyx_k_86), 0, 0, 1, 0},
- {&__pyx_kp_s_87, __pyx_k_87, sizeof(__pyx_k_87), 0, 0, 1, 0},
+ {&__pyx_n_s_87, __pyx_k_87, sizeof(__pyx_k_87), 0, 0, 1, 1},
{&__pyx_kp_s_88, __pyx_k_88, sizeof(__pyx_k_88), 0, 0, 1, 0},
{&__pyx_kp_s_89, __pyx_k_89, sizeof(__pyx_k_89), 0, 0, 1, 0},
- {&__pyx_n_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 1},
- {&__pyx_kp_s_90, __pyx_k_90, sizeof(__pyx_k_90), 0, 0, 1, 0},
+ {&__pyx_kp_b_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 0, 0},
+ {&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
+ {&__pyx_n_s_90, __pyx_k_90, sizeof(__pyx_k_90), 0, 0, 1, 1},
{&__pyx_kp_s_91, __pyx_k_91, sizeof(__pyx_k_91), 0, 0, 1, 0},
{&__pyx_kp_s_92, __pyx_k_92, sizeof(__pyx_k_92), 0, 0, 1, 0},
- {&__pyx_kp_s_93, __pyx_k_93, sizeof(__pyx_k_93), 0, 0, 1, 0},
- {&__pyx_kp_s_94, __pyx_k_94, sizeof(__pyx_k_94), 0, 0, 1, 0},
- {&__pyx_kp_s_95, __pyx_k_95, sizeof(__pyx_k_95), 0, 0, 1, 0},
- {&__pyx_kp_s_96, __pyx_k_96, sizeof(__pyx_k_96), 0, 0, 1, 0},
- {&__pyx_kp_s_97, __pyx_k_97, sizeof(__pyx_k_97), 0, 0, 1, 0},
- {&__pyx_kp_s_98, __pyx_k_98, sizeof(__pyx_k_98), 0, 0, 1, 0},
- {&__pyx_kp_s_99, __pyx_k_99, sizeof(__pyx_k_99), 0, 0, 1, 0},
+ {&__pyx_n_s_93, __pyx_k_93, sizeof(__pyx_k_93), 0, 0, 1, 1},
+ {&__pyx_n_s_97, __pyx_k_97, sizeof(__pyx_k_97), 0, 0, 1, 1},
+ {&__pyx_n_s_98, __pyx_k_98, sizeof(__pyx_k_98), 0, 0, 1, 1},
+ {&__pyx_kp_b__0, __pyx_k__0, sizeof(__pyx_k__0), 0, 0, 0, 0},
{&__pyx_kp_s__0, __pyx_k__0, sizeof(__pyx_k__0), 0, 0, 1, 0},
{&__pyx_n_s__ACGTN, __pyx_k__ACGTN, sizeof(__pyx_k__ACGTN), 0, 0, 1, 1},
{&__pyx_n_s__ALT, __pyx_k__ALT, sizeof(__pyx_k__ALT), 0, 0, 1, 1},
{&__pyx_n_s__NT_UNKNOWN, __pyx_k__NT_UNKNOWN, sizeof(__pyx_k__NT_UNKNOWN), 0, 0, 1, 1},
{&__pyx_n_s__NotImplementedError, __pyx_k__NotImplementedError, sizeof(__pyx_k__NotImplementedError), 0, 0, 1, 1},
{&__pyx_n_s__Number, __pyx_k__Number, sizeof(__pyx_k__Number), 0, 0, 1, 1},
+ {&__pyx_n_b__PASS, __pyx_k__PASS, sizeof(__pyx_k__PASS), 0, 0, 0, 1},
{&__pyx_n_s__PASS, __pyx_k__PASS, sizeof(__pyx_k__PASS), 0, 0, 1, 1},
{&__pyx_n_s__POS, __pyx_k__POS, sizeof(__pyx_k__POS), 0, 0, 1, 1},
{&__pyx_n_s__POS_NOT_NUMERICAL, __pyx_k__POS_NOT_NUMERICAL, sizeof(__pyx_k__POS_NOT_NUMERICAL), 0, 0, 1, 1},
{&__pyx_n_s__alt, __pyx_k__alt, sizeof(__pyx_k__alt), 0, 0, 1, 1},
{&__pyx_n_s__alt1, __pyx_k__alt1, sizeof(__pyx_k__alt1), 0, 0, 1, 1},
{&__pyx_n_s__alt2, __pyx_k__alt2, sizeof(__pyx_k__alt2), 0, 0, 1, 1},
+ {&__pyx_n_s__append, __pyx_k__append, sizeof(__pyx_k__append), 0, 0, 1, 1},
{&__pyx_n_s__bisect, __pyx_k__bisect, sizeof(__pyx_k__bisect), 0, 0, 1, 1},
{&__pyx_n_s__buffer, __pyx_k__buffer, sizeof(__pyx_k__buffer), 0, 0, 1, 1},
{&__pyx_n_s__chrom, __pyx_k__chrom, sizeof(__pyx_k__chrom), 0, 0, 1, 1},
{&__pyx_n_s__convertGT, __pyx_k__convertGT, sizeof(__pyx_k__convertGT), 0, 0, 1, 1},
{&__pyx_n_s__convertGTback, __pyx_k__convertGTback, sizeof(__pyx_k__convertGTback), 0, 0, 1, 1},
{&__pyx_n_s__copy, __pyx_k__copy, sizeof(__pyx_k__copy), 0, 0, 1, 1},
+ {&__pyx_n_s__cvcf, __pyx_k__cvcf, sizeof(__pyx_k__cvcf), 0, 0, 1, 1},
{&__pyx_n_s__data, __pyx_k__data, sizeof(__pyx_k__data), 0, 0, 1, 1},
{&__pyx_n_s__datagenerator, __pyx_k__datagenerator, sizeof(__pyx_k__datagenerator), 0, 0, 1, 1},
{&__pyx_n_s__deepcopy, __pyx_k__deepcopy, sizeof(__pyx_k__deepcopy), 0, 0, 1, 1},
{&__pyx_n_s__parse_formatdata, __pyx_k__parse_formatdata, sizeof(__pyx_k__parse_formatdata), 0, 0, 1, 1},
{&__pyx_n_s__parse_header, __pyx_k__parse_header, sizeof(__pyx_k__parse_header), 0, 0, 1, 1},
{&__pyx_n_s__parse_heading, __pyx_k__parse_heading, sizeof(__pyx_k__parse_heading), 0, 0, 1, 1},
+ {&__pyx_n_s__parse_regions, __pyx_k__parse_regions, sizeof(__pyx_k__parse_regions), 0, 0, 1, 1},
{&__pyx_n_s__parser, __pyx_k__parser, sizeof(__pyx_k__parser), 0, 0, 1, 1},
{&__pyx_n_s__pos, __pyx_k__pos, sizeof(__pyx_k__pos), 0, 0, 1, 1},
{&__pyx_n_s__pos1, __pyx_k__pos1, sizeof(__pyx_k__pos1), 0, 0, 1, 1},
return -1;
}
-static int __Pyx_InitGlobals(void) {
- #if PY_VERSION_HEX < 0x02040000
- if (unlikely(__Pyx_Py23SetsImport() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_2 = PyInt_FromLong(2); if (unlikely(!__pyx_int_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_3 = PyInt_FromLong(3); if (unlikely(!__pyx_int_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_4 = PyInt_FromLong(4); if (unlikely(!__pyx_int_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_5 = PyInt_FromLong(5); if (unlikely(!__pyx_int_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_6 = PyInt_FromLong(6); if (unlikely(!__pyx_int_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_7 = PyInt_FromLong(7); if (unlikely(!__pyx_int_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_8 = PyInt_FromLong(8); if (unlikely(!__pyx_int_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_9 = PyInt_FromLong(9); if (unlikely(!__pyx_int_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_10 = PyInt_FromLong(10); if (unlikely(!__pyx_int_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_11 = PyInt_FromLong(11); if (unlikely(!__pyx_int_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_12 = PyInt_FromLong(12); if (unlikely(!__pyx_int_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_13 = PyInt_FromLong(13); if (unlikely(!__pyx_int_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_14 = PyInt_FromLong(14); if (unlikely(!__pyx_int_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_15 = PyInt_FromLong(15); if (unlikely(!__pyx_int_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_16 = PyInt_FromLong(16); if (unlikely(!__pyx_int_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_17 = PyInt_FromLong(17); if (unlikely(!__pyx_int_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_18 = PyInt_FromLong(18); if (unlikely(!__pyx_int_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_19 = PyInt_FromLong(19); if (unlikely(!__pyx_int_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_20 = PyInt_FromLong(20); if (unlikely(!__pyx_int_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_21 = PyInt_FromLong(21); if (unlikely(!__pyx_int_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_22 = PyInt_FromLong(22); if (unlikely(!__pyx_int_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_23 = PyInt_FromLong(23); if (unlikely(!__pyx_int_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_24 = PyInt_FromLong(24); if (unlikely(!__pyx_int_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_25 = PyInt_FromLong(25); if (unlikely(!__pyx_int_25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_26 = PyInt_FromLong(26); if (unlikely(!__pyx_int_26)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_27 = PyInt_FromLong(27); if (unlikely(!__pyx_int_27)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_28 = PyInt_FromLong(28); if (unlikely(!__pyx_int_28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_29 = PyInt_FromLong(29); if (unlikely(!__pyx_int_29)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_30 = PyInt_FromLong(30); if (unlikely(!__pyx_int_30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_33 = PyInt_FromLong(33); if (unlikely(!__pyx_int_33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_40 = PyInt_FromLong(40); if (unlikely(!__pyx_int_40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_100 = PyInt_FromLong(100); if (unlikely(!__pyx_int_100)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_3000000000 = PyInt_FromString((char *)"3000000000", 0, 0); if (unlikely(!__pyx_int_3000000000)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+ * #
+ */
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "pysam/ctabix.pxd":2
+ /* "ctabix.pxd":2
*
* cdef extern from "string.h": # <<<<<<<<<<<<<<
* ctypedef int size_t
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
if (__pyx_m) {
__Pyx_AddTraceback("init cvcf");
Py_DECREF(__pyx_m); __pyx_m = 0;
return result;
}
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name,
- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AS_STRING(kw_name));
- #endif
-}
-
static void __Pyx_RaiseArgtupleInvalid(
const char* func_name,
int exact,
func_name, more_or_less, num_expected, number, num_found);
}
+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name,
+ PyObject* kw_name)
+{
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION >= 3
+ "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
+ #else
+ "%s() got multiple values for keyword argument '%s'", func_name,
+ PyString_AS_STRING(kw_name));
+ #endif
+}
+
static int __Pyx_ParseOptionalKeywords(
PyObject *kwds,
PyObject **argnames[],
}
-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
- PyObject *local_type, *local_value, *local_tb;
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- local_type = tstate->curexc_type;
- local_value = tstate->curexc_value;
- local_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- PyErr_NormalizeException(&local_type, &local_value, &local_tb);
- if (unlikely(tstate->curexc_type))
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
+ PyObject *local_type, *local_value, *local_tb;
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+ local_type = tstate->curexc_type;
+ local_value = tstate->curexc_value;
+ local_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+ PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+ if (unlikely(tstate->curexc_type))
+ goto bad;
+ #if PY_MAJOR_VERSION >= 3
+ if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
+ goto bad;
+ #endif
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+ Py_INCREF(local_type);
+ Py_INCREF(local_value);
+ Py_INCREF(local_tb);
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = local_type;
+ tstate->exc_value = local_value;
+ tstate->exc_traceback = local_tb;
+ /* Make sure tstate is in a consistent state when we XDECREF
+ these objects (XDECREF may run arbitrary code). */
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+ return 0;
+bad:
+ *type = 0;
+ *value = 0;
+ *tb = 0;
+ Py_XDECREF(local_type);
+ Py_XDECREF(local_value);
+ Py_XDECREF(local_tb);
+ return -1;
+}
+
+
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+
+ tmp_type = tstate->curexc_type;
+ tmp_value = tstate->curexc_value;
+ tmp_tb = tstate->curexc_traceback;
+ tstate->curexc_type = type;
+ tstate->curexc_value = value;
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->curexc_type;
+ *value = tstate->curexc_value;
+ *tb = tstate->curexc_traceback;
+
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+}
+
+
+#if PY_MAJOR_VERSION < 3
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ Py_XINCREF(type);
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ /* First, check the traceback argument, replacing None with NULL. */
+ if (tb == Py_None) {
+ Py_DECREF(tb);
+ tb = 0;
+ }
+ else if (tb != NULL && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ /* Next, replace a missing value with None */
+ if (value == NULL) {
+ value = Py_None;
+ Py_INCREF(value);
+ }
+ #if PY_VERSION_HEX < 0x02050000
+ if (!PyClass_Check(type))
+ #else
+ if (!PyType_Check(type))
+ #endif
+ {
+ /* Raising an instance. The value should be a dummy. */
+ if (value != Py_None) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ /* Normalize to raise <class>, <instance> */
+ Py_DECREF(value);
+ value = type;
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+ Py_INCREF(type);
+ }
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
+ #else
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ #endif
+ }
+
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+
+#else /* Python 3+ */
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ if (tb == Py_None) {
+ tb = 0;
+ } else if (tb && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
goto bad;
- #if PY_MAJOR_VERSION >= 3
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
+ }
+ if (value == Py_None)
+ value = 0;
+
+ if (PyExceptionInstance_Check(type)) {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto bad;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(value);
+ } else if (!PyExceptionClass_Check(type)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
goto bad;
- #endif
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
- Py_INCREF(local_type);
- Py_INCREF(local_value);
- Py_INCREF(local_tb);
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = local_type;
- tstate->exc_value = local_value;
- tstate->exc_traceback = local_tb;
- /* Make sure tstate is in a consistent state when we XDECREF
- these objects (XDECREF may run arbitrary code). */
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
- return 0;
+ }
+
+ PyErr_SetObject(type, value);
+
+ if (tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* tmp_tb = tstate->curexc_traceback;
+ if (tb != tmp_tb) {
+ Py_INCREF(tb);
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_tb);
+ }
+ }
+
bad:
- *type = 0;
- *value = 0;
- *tb = 0;
- Py_XDECREF(local_type);
- Py_XDECREF(local_value);
- Py_XDECREF(local_tb);
- return -1;
+ return;
}
-
+#endif
static double __Pyx__PyObject_AsDouble(PyObject* obj) {
PyObject* float_value;
return module;
}
-static PyObject *__Pyx_CreateClass(
- PyObject *bases, PyObject *dict, PyObject *name, const char *modname)
-{
- PyObject *py_modname;
- PyObject *result = 0;
-
- #if PY_MAJOR_VERSION < 3
- py_modname = PyString_FromString(modname);
- #else
- py_modname = PyUnicode_FromString(modname);
- #endif
- if (!py_modname)
- goto bad;
- if (PyDict_SetItemString(dict, "__module__", py_modname) < 0)
- goto bad;
- #if PY_MAJOR_VERSION < 3
- result = PyClass_New(bases, dict, name);
- #else
- result = PyObject_CallFunctionObjArgs((PyObject *)&PyType_Type, name, bases, dict, NULL);
- #endif
-bad:
- Py_XDECREF(py_modname);
- return result;
-}
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
-
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
+static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
+ PyObject *metaclass;
+ /* Default metaclass */
+#if PY_MAJOR_VERSION < 3
+ if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
+ PyObject *base = PyTuple_GET_ITEM(bases, 0);
+ metaclass = PyObject_GetAttrString(base, "__class__");
+ if (!metaclass) {
+ PyErr_Clear();
+ metaclass = (PyObject*) Py_TYPE(base);
+ }
+ } else {
+ metaclass = (PyObject *) &PyClass_Type;
+ }
+#else
+ if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
+ PyObject *base = PyTuple_GET_ITEM(bases, 0);
+ metaclass = (PyObject*) Py_TYPE(base);
+ } else {
+ metaclass = (PyObject *) &PyType_Type;
+ }
+#endif
+ Py_INCREF(metaclass);
+ return metaclass;
}
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
-
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-}
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
+ PyObject *modname) {
+ PyObject *result;
+ PyObject *metaclass;
+ if (PyDict_SetItemString(dict, "__module__", modname) < 0)
+ return NULL;
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- /* First, check the traceback argument, replacing None with NULL. */
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- /* Next, replace a missing value with None */
- if (value == NULL) {
- value = Py_None;
- Py_INCREF(value);
- }
- #if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
- #else
- if (!PyType_Check(type))
- #endif
- {
- /* Raising an instance. The value should be a dummy. */
- if (value != Py_None) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- /* Normalize to raise <class>, <instance> */
- Py_DECREF(value);
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
+ /* Python2 __metaclass__ */
+ metaclass = PyDict_GetItemString(dict, "__metaclass__");
+ if (metaclass) {
+ Py_INCREF(metaclass);
+ } else {
+ metaclass = __Pyx_FindPy2Metaclass(bases);
}
-
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
+ result = PyObject_CallFunctionObjArgs(metaclass, name, bases, dict, NULL);
+ Py_DECREF(metaclass);
+ return result;
}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
+static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module) {
+ __pyx_binding_PyCFunctionType_object *op = PyObject_GC_New(__pyx_binding_PyCFunctionType_object, __pyx_binding_PyCFunctionType);
+ if (op == NULL)
+ return NULL;
+ op->func.m_ml = ml;
+ Py_XINCREF(self);
+ op->func.m_self = self;
+ Py_XINCREF(module);
+ op->func.m_module = module;
+ PyObject_GC_Track(op);
+ return (PyObject *)op;
+}
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
+static void __pyx_binding_PyCFunctionType_dealloc(__pyx_binding_PyCFunctionType_object *m) {
+ PyObject_GC_UnTrack(m);
+ Py_XDECREF(m->func.m_self);
+ Py_XDECREF(m->func.m_module);
+ PyObject_GC_Del(m);
+}
- PyErr_SetObject(type, value);
+static PyObject *__pyx_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) {
+ if (obj == Py_None)
+ obj = NULL;
+ return PyMethod_New(func, obj, type);
+}
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
+static int __pyx_binding_PyCFunctionType_init(void) {
+ __pyx_binding_PyCFunctionType_type = PyCFunction_Type;
+ __pyx_binding_PyCFunctionType_type.tp_name = __Pyx_NAMESTR("cython_binding_builtin_function_or_method");
+ __pyx_binding_PyCFunctionType_type.tp_dealloc = (destructor)__pyx_binding_PyCFunctionType_dealloc;
+ __pyx_binding_PyCFunctionType_type.tp_descr_get = __pyx_binding_PyCFunctionType_descr_get;
+ if (PyType_Ready(&__pyx_binding_PyCFunctionType_type) < 0) {
+ return -1;
}
+ __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type;
+ return 0;
-bad:
- return;
}
-#endif
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
if (!result)
goto bad;
if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
+ PyErr_Format(PyExc_TypeError,
"%s.%s is not a type object",
module_name, class_name);
goto bad;
}
if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
+ PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
#if PY_VERSION_HEX < 0x02050000
#endif
}
else if (((PyTypeObject *)result)->tp_basicsize != size) {
- PyErr_Format(PyExc_ValueError,
+ PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
goto bad;
}
#endif
-static int __Pyx_GetVtable(PyObject *dict, void *vtabptr) {
+static void* __Pyx_GetVtable(PyObject *dict) {
+ void* ptr;
PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
if (!ob)
goto bad;
#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- *(void **)vtabptr = PyCapsule_GetPointer(ob, 0);
+ ptr = PyCapsule_GetPointer(ob, 0);
#else
- *(void **)vtabptr = PyCObject_AsVoidPtr(ob);
+ ptr = PyCObject_AsVoidPtr(ob);
#endif
- if (!*(void **)vtabptr)
- goto bad;
+ if (!ptr && !PyErr_Occurred())
+ PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
Py_DECREF(ob);
- return 0;
+ return ptr;
bad:
Py_XDECREF(ob);
- return -1;
+ return NULL;
}
static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
// taken from bam_index.c
// The order of the following declarations is important.
// #######################################################
+#define BAM_MAX_BIN 37450 // =(8^6-1)/7+1
+// initialize hashes
typedef struct
{
uint64_t u, v;
#define pair64_lt(a,b) ((a).u < (b).u)
+KSORT_INIT(myoff, pair64_t, pair64_lt);
+
typedef struct {
uint32_t m, n;
pair64_t *list;
uint64_t *offset;
} bam_lidx_t;
-KSORT_INIT(my_off, pair64_t, pair64_lt);
-KHASH_MAP_INIT_INT(my_i, bam_binlist_t);
+
+// initialize hashes ('i' and 's' are idenditifiers)
+KHASH_MAP_INIT_INT(i, bam_binlist_t);
KHASH_MAP_INIT_STR(s, int)
struct __bam_index_t
{
int32_t n;
- khash_t(my_i) **index;
+ uint64_t n_no_coor; // unmapped reads without coordinate
+ khash_t(i) **index;
bam_lidx_t *index2;
};
bam_pileup1_t *pu;
int flag_mask;
};
-
+
static mempool_t *mp_init()
{
mempool_t *mp;
errmod_t *em;
} bmc_aux_t;
-uint32_t pysam_glf_depth( glf1_t * g )
+// Return number of mapped reads on tid.
+// If tid < 0, return mapped reads without a coordinate (0)
+uint32_t pysam_get_mapped( const bam_index_t *idx, const int tid )
{
- return g->depth;
-}
-
-void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c )
-{
- int x = 0;
- fprintf(stderr,
- "glf: ref_base=%i, max_mapQ=%i, min_lk=%i, depth=%i",
- g->ref_base,
- g->max_mapQ,
- g->min_lk,
- g->depth );
-
- for (x = 0; x < 10; ++x)
- fprintf(stderr, ", lk%x=%i, ", x, g->lk[x]);
-
- fprintf(stderr,
- "maqcns: het_rate=%f, theta=%f, n_hap=%i, cap_mapQ=%i, errmod=%i, min_baseQ=%i, eta=%f, q_r=%f, aux_max=%i",
- c->het_rate,
- c->theta,
- c->n_hap,
- c->cap_mapQ,
- c->errmod,
- c->min_baseQ,
- c->eta,
- c->q_r,
- c->aux->max);
-
- for (x = 0; x < c->aux->max; ++x)
+ if (tid >= 0)
{
- fprintf(stderr, ", info-%i=%i ", x, c->aux->info[x]);
- if (c->aux->info[x] == 0) break;
+ khint_t k;
+ khash_t(i) *h = idx->index[tid];
+ k = kh_get(i, h, BAM_MAX_BIN);
+
+ if (k != kh_end(h))
+ return kh_val(h, k).list[1].u;
+ else
+ return 0;
}
-
- for (x = 0; x < c->aux->max; ++x)
+
+ return 0;
+}
+
+uint32_t pysam_get_unmapped( const bam_index_t *idx, const int tid )
+{
+
+ if (tid >= 0)
{
- fprintf(stderr, ", info16-%i=%i ", x, c->aux->info16[x]);
- if (c->aux->info16[x] == 0) break;
+ khint_t k;
+ khash_t(i) *h = idx->index[tid];
+ k = kh_get(i, h, BAM_MAX_BIN);
+
+ if (k != kh_end(h))
+ return kh_val(h, k).list[1].v;
+ else
+ return 0;
}
+
+ return idx->n_no_coor;
}
+/* uint32_t pysam_glf_depth( glf1_t * g ) */
+/* { */
+/* return g->depth; */
+/* } */
+
+
+/* void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c ) */
+/* { */
+/* int x = 0; */
+/* fprintf(stderr, */
+/* "glf: ref_base=%i, max_mapQ=%i, min_lk=%i, depth=%i", */
+/* g->ref_base, */
+/* g->max_mapQ, */
+/* g->min_lk, */
+/* g->depth ); */
+
+/* for (x = 0; x < 10; ++x) */
+/* fprintf(stderr, ", lk%x=%i, ", x, g->lk[x]); */
+
+/* fprintf(stderr, */
+/* "maqcns: het_rate=%f, theta=%f, n_hap=%i, cap_mapQ=%i, errmod=%i, min_baseQ=%i, eta=%f, q_r=%f, aux_max=%i", */
+/* c->het_rate, */
+/* c->theta, */
+/* c->n_hap, */
+/* c->cap_mapQ, */
+/* c->errmod, */
+/* c->min_baseQ, */
+/* c->eta, */
+/* c->q_r, */
+/* c->aux->max); */
+
+/* for (x = 0; x < c->aux->max; ++x) */
+/* { */
+/* fprintf(stderr, ", info-%i=%i ", x, c->aux->info[x]); */
+/* if (c->aux->info[x] == 0) break; */
+/* } */
+
+/* for (x = 0; x < c->aux->max; ++x) */
+/* { */
+/* fprintf(stderr, ", info16-%i=%i ", x, c->aux->info16[x]); */
+/* if (c->aux->info16[x] == 0) break; */
+/* } */
+/* } */
+
// command line within python.
// taken from the main function in bamtk.c
// added code to reset getopt
-extern int main_samview(int argc, char *argv[]);
-extern int main_import(int argc, char *argv[]);
-extern int bam_pileup(int argc, char *argv[]);
-extern int bam_merge(int argc, char *argv[]);
-extern int bam_sort(int argc, char *argv[]);
-extern int bam_index(int argc, char *argv[]);
-extern int faidx_main(int argc, char *argv[]);
-extern int bam_mating(int argc, char *argv[]);
-extern int bam_rmdup(int argc, char *argv[]);
-extern int glf3_view_main(int argc, char *argv[]);
-extern int bam_flagstat(int argc, char *argv[]);
-extern int bam_fillmd(int argc, char *argv[]);
+int bam_taf2baf(int argc, char *argv[]);
+int bam_mpileup(int argc, char *argv[]);
+int bam_merge(int argc, char *argv[]);
+int bam_index(int argc, char *argv[]);
+int bam_sort(int argc, char *argv[]);
+int bam_tview_main(int argc, char *argv[]);
+int bam_mating(int argc, char *argv[]);
+int bam_rmdup(int argc, char *argv[]);
+int bam_flagstat(int argc, char *argv[]);
+int bam_fillmd(int argc, char *argv[]);
+int bam_idxstats(int argc, char *argv[]);
+int main_samview(int argc, char *argv[]);
+int main_import(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
+int main_cut_target(int argc, char *argv[]);
+int main_phase(int argc, char *argv[]);
+int main_cat(int argc, char *argv[]);
+int main_depth(int argc, char *argv[]);
+int main_bam2fq(int argc, char *argv[]);
+int faidx_main(int argc, char *argv[]);
int pysam_dispatch(int argc, char *argv[] )
{
#endif
#endif
- // reset getop
+ // reset getopt
optind = 1;
if (argc < 2) return 1;
if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
- else if (strcmp(argv[1], "pileup") == 0) return bam_pileup(argc-1, argv+1);
+ else if (strcmp(argv[1], "mpileup") == 0) return bam_mpileup(argc-1, argv+1);
else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
- else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
+ else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
+ else if (strcmp(argv[1], "idxstats") == 0) return bam_idxstats(argc-1, argv+1);
else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
- else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
-
+ else if (strcmp(argv[1], "reheader") == 0) return main_reheader(argc-1, argv+1);
+ else if (strcmp(argv[1], "cat") == 0) return main_cat(argc-1, argv+1);
+ else if (strcmp(argv[1], "targetcut") == 0) return main_cut_target(argc-1, argv+1);
+ else if (strcmp(argv[1], "phase") == 0) return main_phase(argc-1, argv+1);
+ else if (strcmp(argv[1], "depth") == 0) return main_depth(argc-1, argv+1);
+ else if (strcmp(argv[1], "bam2fq") == 0) return main_bam2fq(argc-1, argv+1);
+
#if _CURSES_LIB != 0
else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
#endif
// translate a reference string *s* to a tid
int pysam_reference2tid( bam_header_t *header, const char * s );
+// return number of mapped reads for tid
+uint32_t pysam_get_mapped( const bam_index_t *idx, const int tid );
+
+// return number of unmapped reads for tid
+uint32_t pysam_get_unmapped( const bam_index_t *idx, const int tid );
+
// debugging functions
-#include "glf.h"
-uint32_t pysam_glf_depth( glf1_t * g);
+/* #include "glf.h" */
+/* uint32_t pysam_glf_depth( glf1_t * g); */
-#include "bam_maqcns.h"
-void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c );
+/* #include "bam_maqcns.h" */
+/* void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c ); */
#endif
# pysam versioning information
-__version__ = "0.5"
+__version__ = "0.6"
-__samtools_version__ = "0.1.16"
+__samtools_version__ = "0.1.18"
__tabix_version__ = "0.2.5"
int32_t l = 0;
for (k = 0; k < c->n_cigar; ++k) {
int op = cigar[k] & BAM_CIGAR_MASK;
- if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP)
+ if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP || op == BAM_CEQUAL || op == BAM_CDIFF)
l += cigar[k] >> BAM_CIGAR_SHIFT;
}
return l;
else {
for (i = 0; i < c->n_cigar; ++i) {
kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
- kputc("MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
+ kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
}
}
kputc('\t', &str);
@copyright Genome Research Ltd.
*/
-#define BAM_VERSION "0.1.16 (r963:234)"
+#define BAM_VERSION "0.1.18 (r982:295)"
#include <stdint.h>
#include <stdlib.h>
/*
CIGAR operations.
*/
-/*! @abstract CIGAR: match */
+/*! @abstract CIGAR: M = match or mismatch*/
#define BAM_CMATCH 0
-/*! @abstract CIGAR: insertion to the reference */
+/*! @abstract CIGAR: I = insertion to the reference */
#define BAM_CINS 1
-/*! @abstract CIGAR: deletion from the reference */
+/*! @abstract CIGAR: D = deletion from the reference */
#define BAM_CDEL 2
-/*! @abstract CIGAR: skip on the reference (e.g. spliced alignment) */
+/*! @abstract CIGAR: N = skip on the reference (e.g. spliced alignment) */
#define BAM_CREF_SKIP 3
-/*! @abstract CIGAR: clip on the read with clipped sequence present in qseq */
+/*! @abstract CIGAR: S = clip on the read with clipped sequence
+ present in qseq */
#define BAM_CSOFT_CLIP 4
-/*! @abstract CIGAR: clip on the read with clipped sequence trimmed off */
+/*! @abstract CIGAR: H = clip on the read with clipped sequence trimmed off */
#define BAM_CHARD_CLIP 5
-/*! @abstract CIGAR: padding */
+/*! @abstract CIGAR: P = padding */
#define BAM_CPAD 6
+/*! @abstract CIGAR: equals = match */
+#define BAM_CEQUAL 7
+/*! @abstract CIGAR: X = mismatch */
+#define BAM_CDIFF 8
/*! @typedef
@abstract Structure for core alignment information.
* negative if we are looking at an indel. */
int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
{
+ static int *var_pos = NULL, nvar_pos = 0;
int i, n, ref4, is_indel, ori_depth = 0;
memset(r, 0, sizeof(bcf_callret1_t));
if (ref_base >= 0) {
r->depth = n; r->ori_depth = ori_depth;
// glfgen
errmod_cal(bca->e, n, 5, bca->bases, r->p);
+
+ // Calculate the Variant Distance Bias (make it optional?)
+ if ( nvar_pos < _n ) {
+ nvar_pos = _n;
+ var_pos = realloc(var_pos,sizeof(int)*nvar_pos);
+ }
+ int alt_dp=0, read_len=0;
+ for (i=0; i<_n; i++) {
+ const bam_pileup1_t *p = pl + i;
+ if ( bam1_seqi(bam1_seq(p->b),p->qpos) == ref_base )
+ continue;
+
+ var_pos[alt_dp] = p->qpos;
+ if ( (bam1_cigar(p->b)[0]&BAM_CIGAR_MASK)==4 )
+ var_pos[alt_dp] -= bam1_cigar(p->b)[0]>>BAM_CIGAR_SHIFT;
+
+ alt_dp++;
+ read_len += p->b->core.l_qseq;
+ }
+ float mvd=0;
+ int j;
+ n=0;
+ for (i=0; i<alt_dp; i++) {
+ for (j=0; j<i; j++) {
+ mvd += abs(var_pos[i] - var_pos[j]);
+ n++;
+ }
+ }
+ r->mvd[0] = n ? mvd/n : 0;
+ r->mvd[1] = alt_dp;
+ r->mvd[2] = alt_dp ? read_len/alt_dp : 0;
+
return r->depth;
}
+
+void calc_vdb(int n, const bcf_callret1_t *calls, bcf_call_t *call)
+{
+ // Variant distance bias. Samples merged by means of DP-weighted average.
+
+ float weight=0, tot_prob=0;
+
+ int i;
+ for (i=0; i<n; i++)
+ {
+ int mvd = calls[i].mvd[0];
+ int dp = calls[i].mvd[1];
+ int read_len = calls[i].mvd[2];
+
+ if ( dp<2 ) continue;
+
+ float prob = 0;
+ if ( dp==2 )
+ {
+ // Exact formula
+ prob = (mvd==0) ? 1.0/read_len : (read_len-mvd)*2.0/read_len/read_len;
+ }
+ else if ( dp==3 )
+ {
+ // Sin, quite accurate approximation
+ float mu = read_len/2.9;
+ prob = mvd>2*mu ? 0 : sin(mvd*3.14/2/mu) / (4*mu/3.14);
+ }
+ else
+ {
+ // Scaled gaussian curve, crude approximation, but behaves well. Using fixed depth for bigger depths.
+ if ( dp>5 )
+ dp = 5;
+ float sigma2 = (read_len/1.9/(dp+1)) * (read_len/1.9/(dp+1));
+ float norm = 1.125*sqrt(2*3.14*sigma2);
+ float mu = read_len/2.9;
+ if ( mvd < mu )
+ prob = exp(-(mvd-mu)*(mvd-mu)/2/sigma2)/norm;
+ else
+ prob = exp(-(mvd-mu)*(mvd-mu)/3.125/sigma2)/norm;
+ }
+
+ //fprintf(pysamerr,"dp=%d mvd=%d read_len=%d -> prob=%f\n", dp,mvd,read_len,prob);
+ tot_prob += prob*dp;
+ weight += dp;
+ }
+ tot_prob = weight ? tot_prob/weight : 1;
+ //fprintf(pysamerr,"prob=%f\n", tot_prob);
+ call->vdb = tot_prob;
+}
+
int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
{
int ref4, i, j, qsum[4];
call->ori_depth += calls[i].ori_depth;
for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
}
+
+ calc_vdb(n, calls, call);
+
return 0;
}
if (i) kputc(',', &s);
kputw(bc->anno[i], &s);
}
+ if ( bc->vdb!=1 )
+ {
+ ksprintf(&s, ";VDB=%.4f", bc->vdb);
+ }
kputc('\0', &s);
// FMT
kputs("PL", &s);
memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
if (bcr) {
uint16_t *dp = (uint16_t*)b->gi[1].data;
- uint8_t *sp = is_SP? b->gi[2].data : 0;
+ int32_t *sp = is_SP? b->gi[2].data : 0;
for (i = 0; i < bc->n; ++i) {
bcf_callret1_t *p = bcr + i;
dp[i] = p->depth < 0xffff? p->depth : 0xffff;
int depth, ori_depth, qsum[4];
int anno[16];
float p[25];
+ int mvd[3]; // mean variant distance, number of variant reads, average read length
} bcf_callret1_t;
typedef struct {
int n, n_alleles, shift, ori_ref, unseen;
int anno[16], depth, ori_depth;
uint8_t *PL;
+ float vdb; // variant distance bias
} bcf_call_t;
#ifdef __cplusplus
#include <string.h>
#include "bam.h"
#include "bam2bcf.h"
-#include "ksort.h"
#include "kaln.h"
#include "kprobaln.h"
#include "khash.h"
KHASH_SET_INIT_STR(rg)
+#include "ksort.h"
+KSORT_INIT_GENERIC(uint32_t)
+
#define MINUS_CONST 0x10000000
#define INDEL_WINDOW_SIZE 50
for (k = 0; k < c->n_cigar; ++k) {
int op = cigar[k] & BAM_CIGAR_MASK;
int l = cigar[k] >> BAM_CIGAR_SHIFT;
- if (op == BAM_CMATCH) {
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
if (c->pos > tpos) return y;
if (x + l > tpos) {
*_tpos = tpos;
int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
const void *rghash)
{
- extern void ks_introsort_uint32_t(int, uint32_t*);
int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
int N, K, l_run, ref_type, n_alt;
char *inscns = 0, *ref2, *query, **ref_sample;
if (n_types == 1 || (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support) { // then skip
free(aux); return -1;
}
+ if (n_types >= 64) {
+ free(aux);
+ if (bam_verbose >= 2)
+ fprintf(pysamerr, "[%s] excessive INDEL alleles at position %d. Skip the position.\n", __func__, pos + 1);
+ return -1;
+ }
types = (int*)calloc(n_types, sizeof(int));
t = 0;
types[t++] = aux[0] - MINUS_CONST;
for (t = 0; t < n_types; ++t)
if (types[t] == 0) break;
ref_type = t; // the index of the reference type (0)
- assert(n_types < 64);
}
{ // calculate left and right boundary
left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0;
for (k = 0; k < b->core.n_cigar; ++k) {
int op = cigar[k]&0xf;
int j, l = cigar[k]>>4;
- if (op == BAM_CMATCH) {
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
for (j = 0; j < l; ++j)
if (x + j >= left && x + j < right)
cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000;
return 0;
}
+int bam_aux_drop_other(bam1_t *b, uint8_t *s)
+{
+ if (s) {
+ uint8_t *p, *aux;
+ aux = bam1_aux(b);
+ p = s - 2;
+ __skip_tag(s);
+ memmove(aux, p, s - p);
+ b->data_len -= b->l_aux - (s - p);
+ b->l_aux = s - p;
+ } else {
+ b->data_len -= b->l_aux;
+ b->l_aux = 0;
+ }
+ return 0;
+}
+
void bam_init_header_hash(bam_header_t *header)
{
if (header->hash == 0) {
return k == kh_end(h)? -1 : kh_value(h, k);
}
-int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end)
+int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *beg, int *end)
{
- char *s, *p;
- int i, l, k;
+ char *s;
+ int i, l, k, name_end;
khiter_t iter;
khash_t(s) *h;
bam_init_header_hash(header);
h = (khash_t(s)*)header->hash;
- l = strlen(str);
- p = s = (char*)malloc(l+1);
- /* squeeze out "," */
- for (i = k = 0; i != l; ++i)
- if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
- s[k] = 0;
- for (i = 0; i != k; ++i) if (s[i] == ':') break;
- s[i] = 0;
- iter = kh_get(s, h, s); /* get the ref_id */
- if (iter == kh_end(h)) { // name not found
- *ref_id = -1; free(s);
- return -1;
- }
- *ref_id = kh_value(h, iter);
- if (i == k) { /* dump the whole sequence */
- *begin = 0; *end = 1<<29; free(s);
- return 0;
- }
- for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
- *begin = atoi(p);
- if (i < k) {
- p = s + i + 1;
- *end = atoi(p);
- } else *end = 1<<29;
- if (*begin > 0) --*begin;
+ *ref_id = *beg = *end = -1;
+ name_end = l = strlen(str);
+ s = (char*)malloc(l+1);
+ // remove space
+ for (i = k = 0; i < l; ++i)
+ if (!isspace(str[i])) s[k++] = str[i];
+ s[k] = 0; l = k;
+ // determine the sequence name
+ for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
+ if (i >= 0) name_end = i;
+ if (name_end < l) { // check if this is really the end
+ int n_hyphen = 0;
+ for (i = name_end + 1; i < l; ++i) {
+ if (s[i] == '-') ++n_hyphen;
+ else if (!isdigit(s[i]) && s[i] != ',') break;
+ }
+ if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
+ s[name_end] = 0;
+ iter = kh_get(s, h, s);
+ if (iter == kh_end(h)) { // cannot find the sequence name
+ iter = kh_get(s, h, str); // try str as the name
+ if (iter == kh_end(h)) {
+ if (bam_verbose >= 2) fprintf(pysamerr, "[%s] fail to determine the sequence name.\n", __func__);
+ free(s); return -1;
+ } else s[name_end] = ':', name_end = l;
+ }
+ } else iter = kh_get(s, h, str);
+ *ref_id = kh_val(h, iter);
+ // parse the interval
+ if (name_end < l) {
+ for (i = k = name_end + 1; i < l; ++i)
+ if (s[i] != ',') s[k++] = s[i];
+ s[k] = 0;
+ *beg = atoi(s + name_end + 1);
+ for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
+ *end = i < k? atoi(s + i + 1) : 1<<29;
+ if (*beg > 0) --*beg;
+ } else *beg = 0, *end = 1<<29;
free(s);
- if (*begin > *end) {
- fprintf(pysamerr, "[bam_parse_region] invalid region.\n");
- return -1;
- }
- return 0;
+ return *beg <= *end? 0 : -1;
}
int32_t bam_aux2i(const uint8_t *s)
#include "kseq.h"
#include "khash.h"
-KSTREAM_INIT(gzFile, gzread, 8192)
+KSTREAM_INIT(gzFile, gzread, 16384)
KHASH_MAP_INIT_STR(ref, uint64_t)
void bam_init_header_hash(bam_header_t *header);
z += str->l + 1;
if (str->s[0] != '*') {
for (s = str->s; *s; ++s) {
- if (isalpha(*s)) ++c->n_cigar;
+ if ((isalpha(*s)) || (*s=='=')) ++c->n_cigar;
else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
}
b->data = alloc_data(b, doff + c->n_cigar * 4);
for (i = 0, s = str->s; i != c->n_cigar; ++i) {
x = strtol(s, &t, 10);
op = toupper(*t);
- if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
+ if (op == 'M') op = BAM_CMATCH;
else if (op == 'I') op = BAM_CINS;
else if (op == 'D') op = BAM_CDEL;
else if (op == 'N') op = BAM_CREF_SKIP;
else if (op == 'S') op = BAM_CSOFT_CLIP;
else if (op == 'H') op = BAM_CHARD_CLIP;
else if (op == 'P') op = BAM_CPAD;
+ else if (op == '=') op = BAM_CEQUAL;
+ else if (op == 'X') op = BAM_CDIFF;
else parse_error(fp->n_lines, "invalid CIGAR operation");
s = t + 1;
bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
z += str->l + 1;
if (strcmp(str->s, "*")) {
c->l_qseq = strlen(str->s);
- if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
- parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
+ if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b))) {
+ fprintf(pysamerr, "Line %ld, sequence length %i vs %i from CIGAR\n",
+ (long)fp->n_lines, c->l_qseq, (int32_t)bam_cigar2qlen(c, bam1_cigar(b)));
+ parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
+ }
p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
memset(p, 0, (c->l_qseq+1)/2);
for (i = 0; i < c->l_qseq; ++i)
else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;
else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++] = (int32_t)strtol(p, &p, 0), ++p;
else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;
- else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++] = (float)strtof(p, &p), ++p;
+ else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++] = (float)strtod(p, &p), ++p;
else parse_error(fp->n_lines, "unrecognized array type");
s += Bsize * n; doff += size;
} else parse_error(fp->n_lines, "unrecognized type");
save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu;
- n_mapped = n_unmapped = n_no_coor = off_end = 0;
+ n_mapped = n_unmapped = n_no_coor = off_end = 0;
off_beg = off_end = bam_tell(fp);
while ((ret = bam_read1(fp, b)) >= 0) {
if (c->tid < 0) ++n_no_coor;
- if (last_tid != c->tid) { // change of chromosomes
+ if (last_tid < c->tid || (last_tid >= 0 && c->tid < 0)) { // change of chromosomes
last_tid = c->tid;
last_bin = 0xffffffffu;
- } else if (last_coor > c->pos) {
+ } else if ((uint32_t)last_tid > (uint32_t)c->tid) {
+ fprintf(pysamerr, "[bam_index_core] the alignment is not sorted (%s): %d-th chr > %d-th chr\n",
+ bam1_qname(b), last_tid+1, c->tid+1);
+ return NULL;
+ } else if ((int32_t)c->tid >= 0 && last_coor > c->pos) {
fprintf(pysamerr, "[bam_index_core] the alignment is not sorted (%s): %u > %u in %d-th chr\n",
bam1_qname(b), last_coor, c->pos, c->tid+1);
- exit(1);
+ return NULL;
}
- if (c->tid >= 0) insert_offset2(&idx->index2[b->core.tid], b, last_off);
+ if (c->tid >= 0 && !(c->flag & BAM_FUNMAP)) insert_offset2(&idx->index2[b->core.tid], b, last_off);
if (c->bin != last_bin) { // then possibly write the binning index
if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
if (bam_tell(fp) <= last_off) {
fprintf(pysamerr, "[bam_index_core] bug in BGZF/RAZF: %llx < %llx\n",
(unsigned long long)bam_tell(fp), (unsigned long long)last_off);
- exit(1);
+ return NULL;
}
if (c->flag & BAM_FUNMAP) ++n_unmapped;
else ++n_mapped;
++n_no_coor;
if (c->tid >= 0 && n_no_coor) {
fprintf(pysamerr, "[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.\n");
- exit(1);
+ return NULL;
}
}
}
}
idx = bam_index_core(fp);
bam_close(fp);
+ if(idx == 0) {
+ fprintf(pysamerr, "[bam_index_build2] fail to index the BAM file.\n");
+ return -1;
+ }
if (_fnidx == 0) {
fnidx = (char*)calloc(strlen(fn) + 5, 1);
strcpy(fnidx, fn); strcat(fnidx, ".bai");
+++ /dev/null
-#include "pysam.h"
-
-#include <math.h>
-#include <assert.h>
-#include "bam.h"
-#include "bam_maqcns.h"
-#include "ksort.h"
-#include "errmod.h"
-#include "kaln.h"
-KSORT_INIT_GENERIC(uint32_t)
-
-#define INDEL_WINDOW_SIZE 50
-#define INDEL_EXT_DEP 0.9
-
-typedef struct __bmc_aux_t {
- int max;
- uint32_t *info;
- uint16_t *info16;
- errmod_t *em;
-} bmc_aux_t;
-
-typedef struct {
- float esum[4], fsum[4];
- uint32_t c[4];
-} glf_call_aux_t;
-
-/*
- P(<b1,b2>) = \theta \sum_{i=1}^{N-1} 1/i
- P(D|<b1,b2>) = \sum_{k=1}^{N-1} p_k 1/2 [(k/N)^n_2(1-k/N)^n_1 + (k/N)^n1(1-k/N)^n_2]
- p_k = 1/k / \sum_{i=1}^{N-1} 1/i
- */
-static void cal_het(bam_maqcns_t *aa)
-{
- int k, n1, n2;
- double sum_harmo; // harmonic sum
- double poly_rate;
-
- free(aa->lhet);
- aa->lhet = (double*)calloc(256 * 256, sizeof(double));
- sum_harmo = 0.0;
- for (k = 1; k <= aa->n_hap - 1; ++k)
- sum_harmo += 1.0 / k;
- for (n1 = 0; n1 < 256; ++n1) {
- for (n2 = 0; n2 < 256; ++n2) {
- long double sum = 0.0;
- double lC = aa->errmod == BAM_ERRMOD_SOAP? 0 : lgamma(n1+n2+1) - lgamma(n1+1) - lgamma(n2+1);
- for (k = 1; k <= aa->n_hap - 1; ++k) {
- double pk = 1.0 / k / sum_harmo;
- double log1 = log((double)k/aa->n_hap);
- double log2 = log(1.0 - (double)k/aa->n_hap);
- sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2));
- }
- aa->lhet[n1<<8|n2] = lC + logl(sum);
- }
- }
- poly_rate = aa->het_rate * sum_harmo;
- aa->q_r = -4.343 * log(2.0 * poly_rate / (1.0 - poly_rate));
-}
-
-/** initialize the helper structure */
-static void cal_coef(bam_maqcns_t *aa)
-{
- int k, n, q;
- long double sum_a[257], b[256], q_c[256], tmp[256], fk2[256];
- double *lC;
-
- if (aa->errmod == BAM_ERRMOD_MAQ2) return; // no need to do the following
- // aa->lhet will be allocated and initialized
- free(aa->fk); free(aa->coef);
- aa->coef = 0;
- aa->fk = (double*)calloc(256, sizeof(double));
- aa->fk[0] = fk2[0] = 1.0;
- for (n = 1; n != 256; ++n) {
- aa->fk[n] = pow(aa->theta, n) * (1.0 - aa->eta) + aa->eta;
- fk2[n] = aa->fk[n>>1]; // this is an approximation, assuming reads equally likely come from both strands
- }
- if (aa->errmod == BAM_ERRMOD_SOAP) return;
- aa->coef = (double*)calloc(256*256*64, sizeof(double));
- lC = (double*)calloc(256 * 256, sizeof(double));
- for (n = 1; n != 256; ++n)
- for (k = 1; k <= n; ++k)
- lC[n<<8|k] = lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1);
- for (q = 1; q != 64; ++q) {
- double e = pow(10.0, -q/10.0);
- double le = log(e);
- double le1 = log(1.0-e);
- for (n = 1; n != 256; ++n) {
- double *coef = aa->coef + (q<<16|n<<8);
- sum_a[n+1] = 0.0;
- for (k = n; k >= 0; --k) { // a_k = \sum_{i=k}^n C^n_k \epsilon^k (1-\epsilon)^{n-k}
- sum_a[k] = sum_a[k+1] + expl(lC[n<<8|k] + k*le + (n-k)*le1);
- b[k] = sum_a[k+1] / sum_a[k];
- if (b[k] > 0.99) b[k] = 0.99;
- }
- for (k = 0; k != n; ++k) // log(\bar\beta_{nk}(\bar\epsilon)^{f_k})
- q_c[k] = -4.343 * fk2[k] * logl(b[k] / e);
- for (k = 1; k != n; ++k) q_c[k] += q_c[k-1]; // \prod_{i=0}^k c_i
- for (k = 0; k <= n; ++k) { // powl() in 64-bit mode seems broken on my Mac OS X 10.4.9
- tmp[k] = -4.343 * logl(1.0 - expl(fk2[k] * logl(b[k])));
- coef[k] = (k? q_c[k-1] : 0) + tmp[k]; // this is the final c_{nk}
- }
- }
- }
- free(lC);
-}
-
-bam_maqcns_t *bam_maqcns_init()
-{
- bam_maqcns_t *bm;
- bm = (bam_maqcns_t*)calloc(1, sizeof(bam_maqcns_t));
- bm->aux = (bmc_aux_t*)calloc(1, sizeof(bmc_aux_t));
- bm->het_rate = 0.001;
- bm->theta = 0.83f;
- bm->n_hap = 2;
- bm->eta = 0.03;
- bm->cap_mapQ = 60;
- bm->min_baseQ = 13;
- return bm;
-}
-
-void bam_maqcns_prepare(bam_maqcns_t *bm)
-{
- if (bm->errmod == BAM_ERRMOD_MAQ2) bm->aux->em = errmod_init(1. - bm->theta);
- cal_coef(bm); cal_het(bm);
-}
-
-void bam_maqcns_destroy(bam_maqcns_t *bm)
-{
- if (bm == 0) return;
- free(bm->lhet); free(bm->fk); free(bm->coef); free(bm->aux->info); free(bm->aux->info16);
- if (bm->aux->em) errmod_destroy(bm->aux->em);
- free(bm->aux); free(bm);
-}
-
-glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam_maqcns_t *bm)
-{
- glf_call_aux_t *b = 0;
- int i, j, k, w[8], c, n;
- glf1_t *g = (glf1_t*)calloc(1, sizeof(glf1_t));
- float p[16], min_p = 1e30;
- uint64_t rms;
-
- g->ref_base = ref_base;
- if (_n == 0) return g;
-
- // construct aux array
- if (bm->aux->max < _n) {
- bm->aux->max = _n;
- kroundup32(bm->aux->max);
- bm->aux->info = (uint32_t*)realloc(bm->aux->info, 4 * bm->aux->max);
- bm->aux->info16 = (uint16_t*)realloc(bm->aux->info16, 2 * bm->aux->max);
- }
- for (i = n = 0, rms = 0; i < _n; ++i) {
- const bam_pileup1_t *p = pl + i;
- uint32_t q, x = 0, qq;
- uint16_t y = 0;
- if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
- q = (uint32_t)bam1_qual(p->b)[p->qpos];
- if (q < bm->min_baseQ) continue;
- x |= (uint32_t)bam1_strand(p->b) << 18 | q << 8 | p->b->core.qual;
- y |= bam1_strand(p->b)<<4;
- if (p->b->core.qual < q) q = p->b->core.qual;
- c = p->b->core.qual < bm->cap_mapQ? p->b->core.qual : bm->cap_mapQ;
- rms += c * c;
- x |= q << 24;
- y |= q << 5;
- qq = bam1_seqi(bam1_seq(p->b), p->qpos);
- q = bam_nt16_nt4_table[qq? qq : ref_base];
- if (!p->is_del && !p->is_refskip && q < 4) x |= 1 << 21 | q << 16, y |= q;
- bm->aux->info16[n] = y;
- bm->aux->info[n++] = x;
- }
- rms = (uint8_t)(sqrt((double)rms / n) + .499);
- if (bm->errmod == BAM_ERRMOD_MAQ2) {
- errmod_cal(bm->aux->em, n, 4, bm->aux->info16, p);
- goto goto_glf;
- }
- ks_introsort(uint32_t, n, bm->aux->info);
- // generate esum and fsum
- b = (glf_call_aux_t*)calloc(1, sizeof(glf_call_aux_t));
- for (k = 0; k != 8; ++k) w[k] = 0;
- for (j = n - 1; j >= 0; --j) { // calculate esum and fsum
- uint32_t info = bm->aux->info[j];
- if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | (info&0xffffff);
- k = info>>16&7;
- if (info>>24 > 0) {
- b->esum[k&3] += bm->fk[w[k]] * (info>>24);
- b->fsum[k&3] += bm->fk[w[k]];
- if (w[k] < 0xff) ++w[k];
- ++b->c[k&3];
- }
- }
- // rescale ->c[]
- for (j = c = 0; j != 4; ++j) c += b->c[j];
- if (c > 255) {
- for (j = 0; j != 4; ++j) b->c[j] = (int)(254.0 * b->c[j] / c + 0.5);
- for (j = c = 0; j != 4; ++j) c += b->c[j];
- }
- if (bm->errmod == BAM_ERRMOD_MAQ) {
- // generate likelihood
- for (j = 0; j != 4; ++j) {
- // homozygous
- float tmp1, tmp3;
- int tmp2, bar_e;
- for (k = 0, tmp1 = tmp3 = 0.0, tmp2 = 0; k != 4; ++k) {
- if (j == k) continue;
- tmp1 += b->esum[k]; tmp2 += b->c[k]; tmp3 += b->fsum[k];
- }
- if (tmp2) {
- bar_e = (int)(tmp1 / tmp3 + 0.5);
- if (bar_e < 4) bar_e = 4; // should not happen
- if (bar_e > 63) bar_e = 63;
- p[j<<2|j] = tmp1 + bm->coef[bar_e<<16|c<<8|tmp2];
- } else p[j<<2|j] = 0.0; // all the bases are j
- // heterozygous
- for (k = j + 1; k < 4; ++k) {
- for (i = 0, tmp2 = 0, tmp1 = tmp3 = 0.0; i != 4; ++i) {
- if (i == j || i == k) continue;
- tmp1 += b->esum[i]; tmp2 += b->c[i]; tmp3 += b->fsum[i];
- }
- if (tmp2) {
- bar_e = (int)(tmp1 / tmp3 + 0.5);
- if (bar_e < 4) bar_e = 4;
- if (bar_e > 63) bar_e = 63;
- p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]] + tmp1 + bm->coef[bar_e<<16|c<<8|tmp2];
- } else p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]]; // all the bases are either j or k
- }
- //
- for (k = 0; k != 4; ++k)
- if (p[j<<2|k] < 0.0) p[j<<2|k] = 0.0;
- }
-
- { // fix p[k<<2|k]
- float max1, max2, min1, min2;
- int max_k, min_k;
- max_k = min_k = -1;
- max1 = max2 = -1.0; min1 = min2 = 1e30;
- for (k = 0; k < 4; ++k) {
- if (b->esum[k] > max1) {
- max2 = max1; max1 = b->esum[k]; max_k = k;
- } else if (b->esum[k] > max2) max2 = b->esum[k];
- }
- for (k = 0; k < 4; ++k) {
- if (p[k<<2|k] < min1) {
- min2 = min1; min1 = p[k<<2|k]; min_k = k;
- } else if (p[k<<2|k] < min2) min2 = p[k<<2|k];
- }
- if (max1 > max2 && (min_k != max_k || min1 + 1.0 > min2))
- p[max_k<<2|max_k] = min1 > 1.0? min1 - 1.0 : 0.0;
- }
- } else if (bm->errmod == BAM_ERRMOD_SOAP) { // apply the SOAP model
- // generate likelihood
- for (j = 0; j != 4; ++j) {
- float tmp;
- // homozygous
- for (k = 0, tmp = 0.0; k != 4; ++k)
- if (j != k) tmp += b->esum[k];
- p[j<<2|j] = tmp;
- // heterozygous
- for (k = j + 1; k < 4; ++k) {
- for (i = 0, tmp = 0.0; i != 4; ++i)
- if (i != j && i != k) tmp += b->esum[i];
- p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]] + tmp;
- }
- }
- }
-
-goto_glf:
- // convert necessary information to glf1_t
- g->ref_base = ref_base; g->max_mapQ = rms;
- g->depth = n > 16777215? 16777215 : n;
- for (j = 0; j != 4; ++j)
- for (k = j; k < 4; ++k)
- if (p[j<<2|k] < min_p) min_p = p[j<<2|k];
- g->min_lk = min_p > 255.0? 255 : (int)(min_p + 0.5);
- for (j = c = 0; j != 4; ++j)
- for (k = j; k < 4; ++k)
- g->lk[c++] = p[j<<2|k]-min_p > 255.0? 255 : (int)(p[j<<2|k]-min_p + 0.5);
-
- free(b);
- return g;
-}
-
-uint32_t glf2cns(const glf1_t *g, int q_r)
-{
- int i, j, k, p[10], ref4;
- uint32_t x = 0;
- ref4 = bam_nt16_nt4_table[g->ref_base];
- for (i = k = 0; i < 4; ++i)
- for (j = i; j < 4; ++j) {
- int prior = (i == ref4 && j == ref4? 0 : i == ref4 || j == ref4? q_r : q_r + 3);
- p[k] = (g->lk[k] + prior)<<4 | i<<2 | j;
- ++k;
- }
- for (i = 1; i < 10; ++i) // insertion sort
- for (j = i; j > 0 && p[j] < p[j-1]; --j)
- k = p[j], p[j] = p[j-1], p[j-1] = k;
- x = (1u<<(p[0]&3) | 1u<<(p[0]>>2&3)) << 28; // the best genotype
- x |= (uint32_t)g->max_mapQ << 16; // rms mapQ
- x |= ((p[1]>>4) - (p[0]>>4) < 256? (p[1]>>4) - (p[0]>>4) : 255) << 8; // consensus Q
- for (k = 0; k < 10; ++k)
- if ((p[k]&0xf) == (ref4<<2|ref4)) break;
- if (k == 10) k = 9;
- x |= (p[k]>>4) - (p[0]>>4) < 256? (p[k]>>4) - (p[0]>>4) : 255; // snp Q
- return x;
-}
-
-uint32_t bam_maqcns_call(int n, const bam_pileup1_t *pl, bam_maqcns_t *bm)
-{
- glf1_t *g;
- uint32_t x;
- if (n) {
- g = bam_maqcns_glfgen(n, pl, 0xf, bm);
- x = g->depth == 0? (0xfU<<28 | 0xfU<<24) : glf2cns(g, (int)(bm->q_r + 0.5));
- free(g);
- } else x = 0xfU<<28 | 0xfU<<24;
- return x;
-}
-
-/************** *****************/
-
-bam_maqindel_opt_t *bam_maqindel_opt_init()
-{
- bam_maqindel_opt_t *mi = (bam_maqindel_opt_t*)calloc(1, sizeof(bam_maqindel_opt_t));
- mi->q_indel = 40;
- mi->r_indel = 0.00015;
- mi->r_snp = 0.001;
- //
- mi->mm_penalty = 3;
- mi->indel_err = 4;
- mi->ambi_thres = 10;
- return mi;
-}
-
-void bam_maqindel_ret_destroy(bam_maqindel_ret_t *mir)
-{
- if (mir == 0) return;
- free(mir->s[0]); free(mir->s[1]); free(mir);
-}
-
-int bam_tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos)
-{
- int k, x = c->pos, y = 0, last_y = 0;
- *_tpos = c->pos;
- for (k = 0; k < c->n_cigar; ++k) {
- int op = cigar[k] & BAM_CIGAR_MASK;
- int l = cigar[k] >> BAM_CIGAR_SHIFT;
- if (op == BAM_CMATCH) {
- if (c->pos > tpos) return y;
- if (x + l > tpos) {
- *_tpos = tpos;
- return y + (tpos - x);
- }
- x += l; y += l;
- last_y = y;
- } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
- else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
- if (x + l > tpos) {
- *_tpos = is_left? x : x + l;
- return y;
- }
- x += l;
- }
- }
- *_tpos = x;
- return last_y;
-}
-
-#define MINUS_CONST 0x10000000
-
-bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref,
- int _n_types, int *_types)
-{
- int i, j, n_types, *types, left, right, max_rd_len = 0;
- bam_maqindel_ret_t *ret = 0;
- // if there is no proposed indel, check if there is an indel from the alignment
- if (_n_types == 0) {
- for (i = 0; i < n; ++i) {
- const bam_pileup1_t *p = pl + i;
- if (!(p->b->core.flag&BAM_FUNMAP) && p->indel != 0) break;
- }
- if (i == n) return 0; // no indel
- }
- { // calculate how many types of indels are available (set n_types and types)
- int m;
- uint32_t *aux;
- aux = (uint32_t*)calloc(n + _n_types + 1, 4);
- m = 0;
- aux[m++] = MINUS_CONST; // zero indel is always a type
- for (i = 0; i < n; ++i) {
- const bam_pileup1_t *p = pl + i;
- if (!(p->b->core.flag&BAM_FUNMAP) && p->indel != 0)
- aux[m++] = MINUS_CONST + p->indel;
- j = bam_cigar2qlen(&p->b->core, bam1_cigar(p->b));
- if (j > max_rd_len) max_rd_len = j;
- }
- if (_n_types) // then also add this to aux[]
- for (i = 0; i < _n_types; ++i)
- if (_types[i]) aux[m++] = MINUS_CONST + _types[i];
- ks_introsort(uint32_t, m, aux);
- // squeeze out identical types
- for (i = 1, n_types = 1; i < m; ++i)
- if (aux[i] != aux[i-1]) ++n_types;
- types = (int*)calloc(n_types, sizeof(int));
- j = 0;
- types[j++] = aux[0] - MINUS_CONST;
- for (i = 1; i < m; ++i) {
- if (aux[i] != aux[i-1])
- types[j++] = aux[i] - MINUS_CONST;
- }
- free(aux);
- }
- { // calculate left and right boundary
- left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0;
- right = pos + INDEL_WINDOW_SIZE;
- if (types[0] < 0) right -= types[0];
- // in case the alignments stand out the reference
- for (i = pos; i < right; ++i)
- if (ref[i] == 0) break;
- right = i;
- }
- { // the core part
- char *ref2, *rs, *inscns = 0;
- int qr_snp, k, l, *score, *pscore, max_ins = types[n_types-1];
- qr_snp = (int)(-4.343 * log(mi->r_snp) + .499);
- if (max_ins > 0) { // get the consensus of inserted sequences
- int *inscns_aux = (int*)calloc(4 * n_types * max_ins, sizeof(int));
- // count occurrences
- for (i = 0; i < n_types; ++i) {
- if (types[i] <= 0) continue; // not insertion
- for (j = 0; j < n; ++j) {
- const bam_pileup1_t *p = pl + j;
- if (!(p->b->core.flag&BAM_FUNMAP) && p->indel == types[i]) {
- for (k = 1; k <= p->indel; ++k) {
- int c = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos + k)];
- if (c < 4) ++inscns_aux[i*max_ins*4 + (k-1)*4 + c];
- }
- }
- }
- }
- // construct the consensus of inserted sequence
- inscns = (char*)calloc(n_types * max_ins, sizeof(char));
- for (i = 0; i < n_types; ++i) {
- for (j = 0; j < types[i]; ++j) {
- int max = 0, max_k = -1, *ia = inscns_aux + i*max_ins*4 + j*4;
- for (k = 0; k < 4; ++k) {
- if (ia[k] > max) {
- max = ia[k];
- max_k = k;
- }
- }
- inscns[i*max_ins + j] = max? 1<<max_k : 15;
- }
- }
- free(inscns_aux);
- }
- // calculate score
- ref2 = (char*)calloc(right - left + types[n_types-1] + 2, 1);
- rs = (char*)calloc(right - left + max_rd_len + types[n_types-1] + 2, 1);
- score = (int*)calloc(n_types * n, sizeof(int));
- pscore = (int*)calloc(n_types * n, sizeof(int));
- for (i = 0; i < n_types; ++i) {
- ka_param_t ap = ka_param_blast;
- ap.band_width = 2 * types[n_types - 1] + 2;
- ap.gap_end_ext = 0;
- // write ref2
- for (k = 0, j = left; j <= pos; ++j)
- ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
- if (types[i] <= 0) j += -types[i];
- else for (l = 0; l < types[i]; ++l)
- ref2[k++] = bam_nt16_nt4_table[(int)inscns[i*max_ins + l]];
- if (types[0] < 0) { // mask deleted sequences
- int jj, tmp = types[i] >= 0? -types[0] : -types[0] + types[i];
- for (jj = 0; jj < tmp && j < right && ref[j]; ++jj, ++j)
- ref2[k++] = 4;
- }
- for (; j < right && ref[j]; ++j)
- ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
- if (j < right) right = j;
- // calculate score for each read
- for (j = 0; j < n; ++j) {
- const bam_pileup1_t *p = pl + j;
- int qbeg, qend, tbeg, tend;
- if (p->b->core.flag & BAM_FUNMAP) continue;
- qbeg = bam_tpos2qpos(&p->b->core, bam1_cigar(p->b), left, 0, &tbeg);
- qend = bam_tpos2qpos(&p->b->core, bam1_cigar(p->b), right, 1, &tend);
- assert(tbeg >= left);
- for (l = qbeg; l < qend; ++l)
- rs[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), l)];
- {
- int x, y, n_acigar, ps;
- uint32_t *acigar;
- ps = 0;
- if (tend - tbeg + types[i] <= 0) {
- score[i*n+j] = -(1<<20);
- pscore[i*n+j] = 1<<20;
- continue;
- }
- acigar = ka_global_core((uint8_t*)ref2 + tbeg - left, tend - tbeg + types[i], (uint8_t*)rs, qend - qbeg, &ap, &score[i*n+j], &n_acigar);
- x = tbeg - left; y = 0;
- for (l = 0; l < n_acigar; ++l) {
- int op = acigar[l]&0xf;
- int len = acigar[l]>>4;
- if (op == BAM_CMATCH) {
- int k;
- for (k = 0; k < len; ++k)
- if (ref2[x+k] != rs[y+k] && ref2[x+k] < 4)
- ps += bam1_qual(p->b)[y+k] < qr_snp? bam1_qual(p->b)[y+k] : qr_snp;
- x += len; y += len;
- } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) {
- if (op == BAM_CINS && l > 0 && l < n_acigar - 1) ps += mi->q_indel * len;
- y += len;
- } else if (op == BAM_CDEL) {
- if (l > 0 && l < n_acigar - 1) ps += mi->q_indel * len;
- x += len;
- }
- }
- pscore[i*n+j] = ps;
- /*if (1) { // for debugging only
- fprintf(pysamerr, "id=%d, pos=%d, type=%d, j=%d, score=%d, psore=%d, %d, %d, %d, %d, %d, ",
- j, pos+1, types[i], j, score[i*n+j], pscore[i*n+j], tbeg, tend, qbeg, qend, mi->q_indel);
- for (l = 0; l < n_acigar; ++l) fprintf(pysamerr, "%d%c", acigar[l]>>4, "MIDS"[acigar[l]&0xf]);
- fprintf(pysamerr, "\n");
- for (l = 0; l < tend - tbeg + types[i]; ++l) fputc("ACGTN"[ref2[l+tbeg-left]], pysamerr);
- fputc('\n', pysamerr);
- for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[rs[l]], pysamerr);
- fputc('\n', pysamerr);
- }*/
- free(acigar);
- }
- }
- }
- { // get final result
- int *sum, max1, max2, max1_i, max2_i;
- // pick up the best two score
- sum = (int*)calloc(n_types, sizeof(int));
- for (i = 0; i < n_types; ++i)
- for (j = 0; j < n; ++j)
- sum[i] += -pscore[i*n+j];
- max1 = max2 = -0x7fffffff; max1_i = max2_i = -1;
- for (i = 0; i < n_types; ++i) {
- if (sum[i] > max1) {
- max2 = max1; max2_i = max1_i; max1 = sum[i]; max1_i = i;
- } else if (sum[i] > max2) {
- max2 = sum[i]; max2_i = i;
- }
- }
- free(sum);
- // write ret
- ret = (bam_maqindel_ret_t*)calloc(1, sizeof(bam_maqindel_ret_t));
- ret->indel1 = types[max1_i]; ret->indel2 = types[max2_i];
- ret->s[0] = (char*)calloc(abs(ret->indel1) + 2, 1);
- ret->s[1] = (char*)calloc(abs(ret->indel2) + 2, 1);
- // write indel sequence
- if (ret->indel1 > 0) {
- ret->s[0][0] = '+';
- for (k = 0; k < ret->indel1; ++k)
- ret->s[0][k+1] = bam_nt16_rev_table[(int)inscns[max1_i*max_ins + k]];
- } else if (ret->indel1 < 0) {
- ret->s[0][0] = '-';
- for (k = 0; k < -ret->indel1 && ref[pos + k + 1]; ++k)
- ret->s[0][k+1] = ref[pos + k + 1];
- } else ret->s[0][0] = '*';
- if (ret->indel2 > 0) {
- ret->s[1][0] = '+';
- for (k = 0; k < ret->indel2; ++k)
- ret->s[1][k+1] = bam_nt16_rev_table[(int)inscns[max2_i*max_ins + k]];
- } else if (ret->indel2 < 0) {
- ret->s[1][0] = '-';
- for (k = 0; k < -ret->indel2 && ref[pos + k + 1]; ++k)
- ret->s[1][k+1] = ref[pos + k + 1];
- } else ret->s[1][0] = '*';
- // write count
- for (i = 0; i < n; ++i) {
- const bam_pileup1_t *p = pl + i;
- if (p->indel == ret->indel1) ++ret->cnt1;
- else if (p->indel == ret->indel2) ++ret->cnt2;
- else ++ret->cnt_anti;
- }
- { // write gl[]
- int tmp, seq_err = 0;
- double x = 1.0;
- tmp = max1_i - max2_i;
- if (tmp < 0) tmp = -tmp;
- for (j = 0; j < tmp + 1; ++j) x *= INDEL_EXT_DEP;
- seq_err = mi->q_indel * (1.0 - x) / (1.0 - INDEL_EXT_DEP);
- ret->gl[0] = ret->gl[1] = 0;
- for (j = 0; j < n; ++j) {
- int s1 = pscore[max1_i*n + j], s2 = pscore[max2_i*n + j];
- //fprintf(pysamerr, "id=%d, %d, %d, %d, %d, %d\n", j, pl[j].b->core.pos+1, types[max1_i], types[max2_i], s1, s2);
- if (s1 > s2) ret->gl[0] += s1 - s2 < seq_err? s1 - s2 : seq_err;
- else ret->gl[1] += s2 - s1 < seq_err? s2 - s1 : seq_err;
- }
- }
- // write cnt_ref and cnt_ambi
- if (max1_i != 0 && max2_i != 0) {
- for (j = 0; j < n; ++j) {
- int diff1 = score[j] - score[max1_i * n + j];
- int diff2 = score[j] - score[max2_i * n + j];
- if (diff1 > 0 && diff2 > 0) ++ret->cnt_ref;
- else if (diff1 == 0 || diff2 == 0) ++ret->cnt_ambi;
- }
- }
- }
- free(score); free(pscore); free(ref2); free(rs); free(inscns);
- }
- { // call genotype
- int q[3], qr_indel = (int)(-4.343 * log(mi->r_indel) + 0.5);
- int min1, min2, min1_i;
- q[0] = ret->gl[0] + (ret->s[0][0] != '*'? 0 : 0) * qr_indel;
- q[1] = ret->gl[1] + (ret->s[1][0] != '*'? 0 : 0) * qr_indel;
- q[2] = n * 3 + (ret->s[0][0] == '*' || ret->s[1][0] == '*'? 1 : 1) * qr_indel;
- min1 = min2 = 0x7fffffff; min1_i = -1;
- for (i = 0; i < 3; ++i) {
- if (q[i] < min1) {
- min2 = min1; min1 = q[i]; min1_i = i;
- } else if (q[i] < min2) min2 = q[i];
- }
- ret->gt = min1_i;
- ret->q_cns = min2 - min1;
- // set q_ref
- if (ret->gt < 2) ret->q_ref = (ret->s[ret->gt][0] == '*')? 0 : q[1-ret->gt] - q[ret->gt] - qr_indel - 3;
- else ret->q_ref = (ret->s[0][0] == '*')? q[0] - q[2] : q[1] - q[2];
- if (ret->q_ref < 0) ret->q_ref = 0;
- }
- free(types);
- return ret;
-}
+++ /dev/null
-#ifndef BAM_MAQCNS_H
-#define BAM_MAQCNS_H
-
-#include "glf.h"
-
-#define BAM_ERRMOD_MAQ2 0
-#define BAM_ERRMOD_MAQ 1
-#define BAM_ERRMOD_SOAP 2
-
-struct __bmc_aux_t;
-
-typedef struct {
- float het_rate, theta;
- int n_hap, cap_mapQ, errmod, min_baseQ;
-
- float eta, q_r;
- double *fk, *coef;
- double *lhet;
- struct __bmc_aux_t *aux;
-} bam_maqcns_t;
-
-typedef struct {
- int q_indel; // indel sequencing error, phred scaled
- float r_indel; // indel prior
- float r_snp; // snp prior
- // hidden parameters, unchangeable from command line
- int mm_penalty, indel_err, ambi_thres;
-} bam_maqindel_opt_t;
-
-typedef struct {
- int indel1, indel2;
- int cnt1, cnt2, cnt_anti;
- int cnt_ref, cnt_ambi;
- char *s[2];
- //
- int gt, gl[2];
- int q_cns, q_ref;
-} bam_maqindel_ret_t;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
- bam_maqcns_t *bam_maqcns_init();
- void bam_maqcns_prepare(bam_maqcns_t *bm);
- void bam_maqcns_destroy(bam_maqcns_t *bm);
- glf1_t *bam_maqcns_glfgen(int n, const bam_pileup1_t *pl, uint8_t ref_base, bam_maqcns_t *bm);
- uint32_t bam_maqcns_call(int n, const bam_pileup1_t *pl, bam_maqcns_t *bm);
- // return: cns<<28 | cns2<<24 | mapQ<<16 | cnsQ<<8 | cnsQ2
- uint32_t glf2cns(const glf1_t *g, int q_r);
-
- bam_maqindel_opt_t *bam_maqindel_opt_init();
- bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref,
- int _n_types, int *_types);
- void bam_maqindel_ret_destroy(bam_maqindel_ret_t*);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
#include "kaln.h"
#include "kprobaln.h"
+#define USE_EQUAL 1
+#define DROP_TAG 2
+#define BIN_QUAL 4
+#define UPDATE_NM 8
+#define UPDATE_MD 16
+#define HASH_QNM 32
+
char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
-void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm)
+int bam_aux_drop_other(bam1_t *b, uint8_t *s);
+
+void bam_fillmd1_core(bam1_t *b, char *ref, int flag, int max_nm)
{
uint8_t *seq = bam1_seq(b);
uint32_t *cigar = bam1_cigar(b);
bam1_core_t *c = &b->core;
int i, x, y, u = 0;
kstring_t *str;
- uint8_t *old_md, *old_nm;
int32_t old_nm_i = -1, nm = 0;
str = (kstring_t*)calloc(1, sizeof(kstring_t));
for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
int j, l = cigar[i]>>4, op = cigar[i]&0xf;
- if (op == BAM_CMATCH) {
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
for (j = 0; j < l; ++j) {
int z = y + j;
int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
if (ref[x+j] == 0) break; // out of boundary
if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
- if (is_equal) seq[z/2] &= (z&1)? 0xf0 : 0x0f;
+ if (flag&USE_EQUAL) seq[z/2] &= (z&1)? 0xf0 : 0x0f;
++u;
} else {
- ksprintf(str, "%d", u);
- kputc(ref[x+j], str);
+ kputw(u, str); kputc(ref[x+j], str);
u = 0; ++nm;
}
}
if (j < l) break;
x += l; y += l;
} else if (op == BAM_CDEL) {
- ksprintf(str, "%d", u);
- kputc('^', str);
+ kputw(u, str); kputc('^', str);
for (j = 0; j < l; ++j) {
if (ref[x+j] == 0) break;
kputc(ref[x+j], str);
x += l;
}
}
- ksprintf(str, "%d", u);
+ kputw(u, str);
// apply max_nm
if (max_nm > 0 && nm >= max_nm) {
for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
int j, l = cigar[i]>>4, op = cigar[i]&0xf;
- if (op == BAM_CMATCH) {
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
for (j = 0; j < l; ++j) {
int z = y + j;
int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
}
}
// update NM
- old_nm = bam_aux_get(b, "NM");
- if (c->flag & BAM_FUNMAP) return;
- if (old_nm) old_nm_i = bam_aux2i(old_nm);
- if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
- else if (nm != old_nm_i) {
- fprintf(pysamerr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm);
- bam_aux_del(b, old_nm);
- bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
+ if (flag & UPDATE_NM) {
+ uint8_t *old_nm = bam_aux_get(b, "NM");
+ if (c->flag & BAM_FUNMAP) return;
+ if (old_nm) old_nm_i = bam_aux2i(old_nm);
+ if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
+ else if (nm != old_nm_i) {
+ fprintf(pysamerr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm);
+ bam_aux_del(b, old_nm);
+ bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
+ }
}
// update MD
- old_md = bam_aux_get(b, "MD");
- if (!old_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
- else {
- int is_diff = 0;
- if (strlen((char*)old_md+1) == str->l) {
- for (i = 0; i < str->l; ++i)
- if (toupper(old_md[i+1]) != toupper(str->s[i]))
- break;
- if (i < str->l) is_diff = 1;
- } else is_diff = 1;
- if (is_diff) {
- fprintf(pysamerr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam1_qname(b), old_md+1, str->s);
- bam_aux_del(b, old_md);
- bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
+ if (flag & UPDATE_MD) {
+ uint8_t *old_md = bam_aux_get(b, "MD");
+ if (c->flag & BAM_FUNMAP) return;
+ if (!old_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
+ else {
+ int is_diff = 0;
+ if (strlen((char*)old_md+1) == str->l) {
+ for (i = 0; i < str->l; ++i)
+ if (toupper(old_md[i+1]) != toupper(str->s[i]))
+ break;
+ if (i < str->l) is_diff = 1;
+ } else is_diff = 1;
+ if (is_diff) {
+ fprintf(pysamerr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam1_qname(b), old_md+1, str->s);
+ bam_aux_del(b, old_md);
+ bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
+ }
}
}
+ // drop all tags but RG
+ if (flag&DROP_TAG) {
+ uint8_t *q = bam_aux_get(b, "RG");
+ bam_aux_drop_other(b, q);
+ }
+ // reduce the resolution of base quality
+ if (flag&BIN_QUAL) {
+ uint8_t *qual = bam1_qual(b);
+ for (i = 0; i < b->core.l_qseq; ++i)
+ if (qual[i] >= 3) qual[i] = qual[i]/10*10 + 7;
+ }
free(str->s); free(str);
}
-void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
+void bam_fillmd1(bam1_t *b, char *ref, int flag)
{
- bam_fillmd1_core(b, ref, is_equal, 0);
+ bam_fillmd1_core(b, ref, flag, 0);
}
int bam_cap_mapQ(bam1_t *b, char *ref, int thres)
mm = q = len = clip_l = clip_q = 0;
for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
int j, l = cigar[i]>>4, op = cigar[i]&0xf;
- if (op == BAM_CMATCH) {
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
for (j = 0; j < l; ++j) {
int z = y + j;
int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
for (k = 0; k < c->n_cigar; ++k) {
int op, l;
op = cigar[k]&0xf; l = cigar[k]>>4;
- if (op == BAM_CMATCH) {
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
if (yb < 0) yb = y;
if (xb < 0) xb = x;
ye = y + l; xe = x + l;
if (!extend_baq) { // in this block, bq[] is capped by base quality qual[]
for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
int op = cigar[k]&0xf, l = cigar[k]>>4;
- if (op == BAM_CMATCH) {
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
for (i = y; i < y + l; ++i) {
if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) bq[i] = 0;
else bq[i] = bq[i] < q[i]? bq[i] : q[i];
left = calloc(c->l_qseq, 1); rght = calloc(c->l_qseq, 1);
for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
int op = cigar[k]&0xf, l = cigar[k]>>4;
- if (op == BAM_CMATCH) {
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
for (i = y; i < y + l; ++i)
bq[i] = ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y))? 0 : q[i];
for (left[y] = bq[y], i = y + 1; i < y + l; ++i)
int bam_fillmd(int argc, char *argv[])
{
- int c, is_equal, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm, is_realn, capQ, baq_flag;
+ int c, flt_flag, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm, is_realn, capQ, baq_flag;
samfile_t *fp, *fpout = 0;
faidx_t *fai;
char *ref = 0, mode_w[8], mode_r[8];
bam1_t *b;
- is_equal = is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = capQ = baq_flag = 0;
+ flt_flag = UPDATE_NM | UPDATE_MD;
+ is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = capQ = baq_flag = 0;
mode_w[0] = mode_r[0] = 0;
strcpy(mode_r, "r"); strcpy(mode_w, "w");
- while ((c = getopt(argc, argv, "EreubSC:n:A")) >= 0) {
+ while ((c = getopt(argc, argv, "EqreuNhbSC:n:Ad")) >= 0) {
switch (c) {
case 'r': is_realn = 1; break;
- case 'e': is_equal = 1; break;
+ case 'e': flt_flag |= USE_EQUAL; break;
+ case 'd': flt_flag |= DROP_TAG; break;
+ case 'q': flt_flag |= BIN_QUAL; break;
+ case 'h': flt_flag |= HASH_QNM; break;
+ case 'N': flt_flag &= ~(UPDATE_MD|UPDATE_NM); break;
case 'b': is_bam_out = 1; break;
case 'u': is_uncompressed = is_bam_out = 1; break;
case 'S': is_sam_in = 1; break;
int q = bam_cap_mapQ(b, ref, capQ);
if (b->core.qual > q) b->core.qual = q;
}
- if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm);
+ if (ref) bam_fillmd1_core(b, ref, flt_flag, max_nm);
}
samwrite(fpout, b);
}
if (s->k == -1) { // never processed
is_head = 1;
if (c->n_cigar == 1) { // just one operation, save a loop
- if (_cop(cigar[0]) == BAM_CMATCH) s->k = 0, s->x = c->pos, s->y = 0;
+ if (_cop(cigar[0]) == BAM_CMATCH || _cop(cigar[0]) == BAM_CEQUAL || _cop(cigar[0]) == BAM_CDIFF) s->k = 0, s->x = c->pos, s->y = 0;
} else { // find the first match or deletion
for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) {
int op = _cop(cigar[k]);
int l = _cln(cigar[k]);
- if (op == BAM_CMATCH || op == BAM_CDEL) break;
+ if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CEQUAL || op == BAM_CDIFF) break;
else if (op == BAM_CREF_SKIP) s->x += l;
else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
}
if (pos - s->x >= l) { // jump to the next operation
assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case
op = _cop(cigar[s->k+1]);
- if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP) { // jump to the next without a loop
- if (_cop(cigar[s->k]) == BAM_CMATCH) s->y += l;
+ if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) { // jump to the next without a loop
+ if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
s->x += l;
++s->k;
- } else { // find the next M/D/N
- if (_cop(cigar[s->k]) == BAM_CMATCH) s->y += l;
+ } else { // find the next M/D/N/=/X
+ if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
s->x += l;
for (k = s->k + 1; k < c->n_cigar; ++k) {
op = _cop(cigar[k]), l = _cln(cigar[k]);
- if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP) break;
+ if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) break;
else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
}
s->k = k;
for (k = s->k + 2; k < c->n_cigar; ++k) {
op2 = _cop(cigar[k]); l2 = _cln(cigar[k]);
if (op2 == BAM_CINS) l3 += l2;
- else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP) break;
+ else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP || op2 == BAM_CEQUAL || op2 == BAM_CDIFF) break;
}
if (l3 > 0) p->indel = l3;
}
}
- if (op == BAM_CMATCH) {
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
p->qpos = s->y + (pos - s->x);
} else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
p->is_del = 1; p->qpos = s->y; // FIXME: distinguish D and N!!!!!
#include <errno.h>
#include "sam.h"
#include "faidx.h"
-#include "bam_maqcns.h"
-#include "khash.h"
-#include "glf.h"
#include "kstring.h"
-typedef int *indel_list_t;
-KHASH_MAP_INIT_INT64(64, indel_list_t)
-
-#define BAM_PLF_SIMPLE 0x01
-#define BAM_PLF_CNS 0x02
-#define BAM_PLF_INDEL_ONLY 0x04
-#define BAM_PLF_GLF 0x08
-#define BAM_PLF_VAR_ONLY 0x10
-#define BAM_PLF_2ND 0x20
-#define BAM_PLF_RANBASE 0x40
-#define BAM_PLF_1STBASE 0x80
-#define BAM_PLF_ALLBASE 0x100
-#define BAM_PLF_READPOS 0x200
-#define BAM_PLF_NOBAQ 0x400
-
-typedef struct {
- bam_header_t *h;
- bam_maqcns_t *c;
- bam_maqindel_opt_t *ido;
- faidx_t *fai;
- khash_t(64) *hash;
- uint32_t format;
- int tid, len, last_pos;
- int mask;
- int capQ_thres, min_baseQ;
- int max_depth; // for indel calling, ignore reads with the depth too high. 0 for unlimited
- char *ref;
- glfFile fp_glf; // for glf output only
-} pu_data_t;
-
-char **__bam_get_lines(const char *fn, int *_n);
-void bam_init_header_hash(bam_header_t *header);
-int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
-
-static khash_t(64) *load_pos(const char *fn, bam_header_t *h)
-{
- char **list;
- int i, j, n, *fields, max_fields;
- khash_t(64) *hash;
- bam_init_header_hash(h);
- list = __bam_get_lines(fn, &n);
- hash = kh_init(64);
- max_fields = 0; fields = 0;
- for (i = 0; i < n; ++i) {
- char *str = list[i];
- int chr, n_fields, ret;
- khint_t k;
- uint64_t x;
- n_fields = ksplit_core(str, 0, &max_fields, &fields);
- if (n_fields < 2) continue;
- chr = bam_get_tid(h, str + fields[0]);
- if (chr < 0) {
- fprintf(pysamerr, "[load_pos] unknown reference sequence name: %s\n", str + fields[0]);
- continue;
- }
- x = (uint64_t)chr << 32 | (atoi(str + fields[1]) - 1);
- k = kh_put(64, hash, x, &ret);
- if (ret == 0) {
- fprintf(pysamerr, "[load_pos] position %s:%s has been loaded.\n", str+fields[0], str+fields[1]);
- continue;
- }
- kh_val(hash, k) = 0;
- if (n_fields > 2) {
- // count
- for (j = 2; j < n_fields; ++j) {
- char *s = str + fields[j];
- if ((*s != '+' && *s != '-') || !isdigit(s[1])) break;
- }
- if (j > 2) { // update kh_val()
- int *q, y, z;
- q = kh_val(hash, k) = (int*)calloc(j - 1, sizeof(int));
- q[0] = j - 2; z = j; y = 1;
- for (j = 2; j < z; ++j)
- q[y++] = atoi(str + fields[j]);
- }
- }
- free(str);
- }
- free(list); free(fields);
- return hash;
-}
-
static inline int printw(int c, FILE *fp)
{
char buf[16];
return 0;
}
-// an analogy to pileup_func() below
-static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
-{
- pu_data_t *d = (pu_data_t*)data;
- bam_maqindel_ret_t *r = 0;
- int rb, *proposed_indels = 0;
- glf1_t *g;
- glf3_t *g3;
-
- if (d->fai == 0) {
- fprintf(pysamerr, "[glt3_func] reference sequence is required for generating GLT. Abort!\n");
- exit(1);
- }
- if (d->hash) { // only output a list of sites
- khint_t k = kh_get(64, d->hash, (uint64_t)tid<<32|pos);
- if (k == kh_end(d->hash)) return 0;
- proposed_indels = kh_val(d->hash, k);
- }
- g3 = glf3_init1();
- if (d->fai && (int)tid != d->tid) {
- if (d->ref) { // then write the end mark
- g3->rtype = GLF3_RTYPE_END;
- glf3_write1(d->fp_glf, g3);
- }
- glf3_ref_write(d->fp_glf, d->h->target_name[tid], d->h->target_len[tid]); // write reference
- free(d->ref);
- d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len);
- d->tid = tid;
- d->last_pos = 0;
- }
- rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N';
- g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c);
- memcpy(g3, g, sizeof(glf1_t));
- g3->rtype = GLF3_RTYPE_SUB;
- g3->offset = pos - d->last_pos;
- d->last_pos = pos;
- glf3_write1(d->fp_glf, g3);
- if (pos < d->len) {
- int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth;
- if (proposed_indels)
- r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
- else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0);
- }
- if (r) { // then write indel line
- int het = 3 * n, min;
- min = het;
- if (min > r->gl[0]) min = r->gl[0];
- if (min > r->gl[1]) min = r->gl[1];
- g3->ref_base = 0;
- g3->rtype = GLF3_RTYPE_INDEL;
- memset(g3->lk, 0, 10);
- g3->lk[0] = r->gl[0] - min < 255? r->gl[0] - min : 255;
- g3->lk[1] = r->gl[1] - min < 255? r->gl[1] - min : 255;
- g3->lk[2] = het - min < 255? het - min : 255;
- g3->offset = 0;
- g3->indel_len[0] = r->indel1;
- g3->indel_len[1] = r->indel2;
- g3->min_lk = min < 255? min : 255;
- g3->max_len = (abs(r->indel1) > abs(r->indel2)? abs(r->indel1) : abs(r->indel2)) + 1;
- g3->indel_seq[0] = strdup(r->s[0]+1);
- g3->indel_seq[1] = strdup(r->s[1]+1);
- glf3_write1(d->fp_glf, g3);
- bam_maqindel_ret_destroy(r);
- }
- free(g);
- glf3_destroy1(g3);
- return 0;
-}
-
static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
{
int j;
if (p->is_tail) putchar('$');
}
-static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
-{
- pu_data_t *d = (pu_data_t*)data;
- bam_maqindel_ret_t *r = 0;
- int i, rb, rms_mapq = -1, *proposed_indels = 0;
- uint64_t rms_aux;
- uint32_t cns = 0;
-
- // if GLF is required, suppress -c completely
- if (d->format & BAM_PLF_GLF) return glt3_func(tid, pos, n, pu, data);
- // if d->hash is initialized, only output the sites in the hash table
- if (d->hash) {
- khint_t k = kh_get(64, d->hash, (uint64_t)tid<<32|pos);
- if (k == kh_end(d->hash)) return 0;
- proposed_indels = kh_val(d->hash, k);
- }
- // update d->ref if necessary
- if (d->fai && (int)tid != d->tid) {
- free(d->ref);
- d->ref = faidx_fetch_seq(d->fai, d->h->target_name[tid], 0, 0x7fffffff, &d->len);
- d->tid = tid;
- }
- rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N';
- // when the indel-only mode is asked for, return if no reads mapped with indels
- if (d->format & BAM_PLF_INDEL_ONLY) {
- for (i = 0; i < n; ++i)
- if (pu[i].indel != 0) break;
- if (i == n) return 0;
- }
- // call the consensus and indel
- if (d->format & BAM_PLF_CNS) { // call consensus
- if (d->format & (BAM_PLF_RANBASE|BAM_PLF_1STBASE)) { // use a random base or the 1st base as the consensus call
- const bam_pileup1_t *p = (d->format & BAM_PLF_1STBASE)? pu : pu + (int)(drand48() * n);
- int q = bam1_qual(p->b)[p->qpos];
- int mapQ = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
- uint32_t b = bam1_seqi(bam1_seq(p->b), p->qpos);
- cns = b<<28 | 0xf<<24 | mapQ<<16 | q<<8;
- } else if (d->format & BAM_PLF_ALLBASE) { // collapse all bases
- uint64_t rmsQ = 0;
- uint32_t b = 0;
- for (i = 0; i < n; ++i) {
- const bam_pileup1_t *p = pu + i;
- int q = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
- b |= bam1_seqi(bam1_seq(p->b), p->qpos);
- rmsQ += q * q;
- }
- rmsQ = (uint64_t)(sqrt((double)rmsQ / n) + .499);
- cns = b<<28 | 0xf<<24 | rmsQ<<16 | 60<<8;
- } else {
- glf1_t *g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c);
- cns = g->depth == 0? (0xfu<<28 | 0xf<<24) : glf2cns(g, (int)(d->c->q_r + .499));
- free(g);
- }
- }
- if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // call indels
- int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth;
- if (proposed_indels) // the first element gives the size of the array
- r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
- else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0);
- }
- // when only variant sites are asked for, test if the site is a variant
- if ((d->format & BAM_PLF_CNS) && (d->format & BAM_PLF_VAR_ONLY)) {
- if (!(bam_nt16_table[rb] != 15 && cns>>28 != 15 && cns>>28 != bam_nt16_table[rb])) { // not a SNP
- if (!(r && (r->gt == 2 || strcmp(r->s[r->gt], "*")))) { // not an indel
- if (r) bam_maqindel_ret_destroy(r);
- return 0;
- }
- }
- }
- // print the first 3 columns
- fputs(d->h->target_name[tid], stdout); putchar('\t');
- printw(pos+1, stdout); putchar('\t'); putchar(rb); putchar('\t');
- // print consensus information if required
- if (d->format & BAM_PLF_CNS) {
- putchar(bam_nt16_rev_table[cns>>28]); putchar('\t');
- printw(cns>>8&0xff, stdout); putchar('\t');
- printw(cns&0xff, stdout); putchar('\t');
- printw(cns>>16&0xff, stdout); putchar('\t');
- }
- // print pileup sequences
- printw(n, stdout); putchar('\t');
- for (i = 0; i < n; ++i)
- pileup_seq(pu + i, pos, d->len, d->ref);
- // finalize rms_mapq
- if (d->format & BAM_PLF_CNS) {
- for (i = rms_aux = 0; i < n; ++i) {
- const bam_pileup1_t *p = pu + i;
- int tmp = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
- rms_aux += tmp * tmp;
- }
- rms_aux = (uint64_t)(sqrt((double)rms_aux / n) + .499);
- if (rms_mapq < 0) rms_mapq = rms_aux;
- }
- putchar('\t');
- // print quality
- for (i = 0; i < n; ++i) {
- const bam_pileup1_t *p = pu + i;
- int c = bam1_qual(p->b)[p->qpos] + 33;
- if (c > 126) c = 126;
- putchar(c);
- }
- if (d->format & BAM_PLF_2ND) { // print 2nd calls and qualities
- const unsigned char *q;
- putchar('\t');
- for (i = 0; i < n; ++i) {
- const bam_pileup1_t *p = pu + i;
- q = bam_aux_get(p->b, "E2");
- putchar(q? q[p->qpos + 1] : 'N');
- }
- putchar('\t');
- for (i = 0; i < n; ++i) {
- const bam_pileup1_t *p = pu + i;
- q = bam_aux_get(p->b, "U2");
- putchar(q? q[p->qpos + 1] : '!');
- }
- }
- // print mapping quality if -s is flagged on the command line
- if (d->format & BAM_PLF_SIMPLE) {
- putchar('\t');
- for (i = 0; i < n; ++i) {
- int c = pu[i].b->core.qual + 33;
- if (c > 126) c = 126;
- putchar(c);
- }
- }
- // print read position
- if (d->format & BAM_PLF_READPOS) {
- putchar('\t');
- for (i = 0; i < n; ++i) {
- int x = pu[i].qpos;
- int l = pu[i].b->core.l_qseq;
- printw(x < l/2? x+1 : -((l-1)-x+1), stdout); putchar(',');
- }
- }
- putchar('\n');
- // print the indel line if r has been calculated. This only happens if:
- // a) -c or -i are flagged, AND b) the reference sequence is available
- if (r) {
- printf("%s\t%d\t*\t", d->h->target_name[tid], pos + 1);
- if (r->gt < 2) printf("%s/%s\t", r->s[r->gt], r->s[r->gt]);
- else printf("%s/%s\t", r->s[0], r->s[1]);
- printf("%d\t%d\t", r->q_cns, r->q_ref);
- printf("%d\t%d\t", rms_mapq, n);
- printf("%s\t%s\t", r->s[0], r->s[1]);
- //printf("%d\t%d\t", r->gl[0], r->gl[1]);
- printf("%d\t%d\t%d\t", r->cnt1, r->cnt2, r->cnt_anti);
- printf("%d\t%d\n", r->cnt_ref, r->cnt_ambi);
- bam_maqindel_ret_destroy(r);
- }
- return 0;
-}
-
-int bam_pileup(int argc, char *argv[])
-{
- int c, is_SAM = 0;
- char *fn_list = 0, *fn_fa = 0, *fn_pos = 0;
- pu_data_t *d = (pu_data_t*)calloc(1, sizeof(pu_data_t));
- d->max_depth = 1024; d->tid = -1; d->mask = BAM_DEF_MASK; d->min_baseQ = 13;
- d->c = bam_maqcns_init();
- d->c->errmod = BAM_ERRMOD_MAQ2; // change the default model
- d->ido = bam_maqindel_opt_init();
- while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:PAQ:C:B")) >= 0) {
- switch (c) {
- case 'Q': d->c->min_baseQ = atoi(optarg); break;
- case 'C': d->capQ_thres = atoi(optarg); break;
- case 'B': d->format |= BAM_PLF_NOBAQ; break;
- case 'a': d->c->errmod = BAM_ERRMOD_SOAP; break;
- case 'A': d->c->errmod = BAM_ERRMOD_MAQ; break;
- case 's': d->format |= BAM_PLF_SIMPLE; break;
- case 't': fn_list = strdup(optarg); break;
- case 'l': fn_pos = strdup(optarg); break;
- case 'f': fn_fa = strdup(optarg); break;
- case 'T': d->c->theta = atof(optarg); break;
- case 'N': d->c->n_hap = atoi(optarg); break;
- case 'r': d->c->het_rate = atof(optarg); d->ido->r_snp = d->c->het_rate; break;
- case 'M': d->c->cap_mapQ = atoi(optarg); break;
- case 'd': d->max_depth = atoi(optarg); break;
- case 'c': d->format |= BAM_PLF_CNS; break;
- case 'i': d->format |= BAM_PLF_INDEL_ONLY; break;
- case 'v': d->format |= BAM_PLF_VAR_ONLY; break;
- case 'm': d->mask = strtol(optarg, 0, 0); break;
- case 'g': d->format |= BAM_PLF_GLF; break;
- case '2': d->format |= BAM_PLF_2ND; break;
- case 'P': d->format |= BAM_PLF_READPOS; break;
- case 'I': d->ido->q_indel = atoi(optarg); break;
- case 'G': d->ido->r_indel = atof(optarg); break;
- case 'S': is_SAM = 1; break;
- case 'R':
- if (strcmp(optarg, "random") == 0) d->format |= BAM_PLF_RANBASE;
- else if (strcmp(optarg, "first") == 0) d->format |= BAM_PLF_1STBASE;
- else if (strcmp(optarg, "all") == 0) d->format |= BAM_PLF_ALLBASE;
- else fprintf(pysamerr, "[bam_pileup] unrecognized -R\n");
- break;
- default: fprintf(pysamerr, "Unrecognizd option '-%c'.\n", c); return 1;
- }
- }
- if (d->c->errmod != BAM_ERRMOD_MAQ2) d->c->theta += 0.02;
- if (d->c->theta > 1.0) d->c->theta = 1.0;
- if (fn_list) is_SAM = 1;
- if (optind == argc) {
- fprintf(pysamerr, "\n");
- fprintf(pysamerr, "Usage: samtools pileup [options] <in.bam>|<in.sam>\n\n");
- fprintf(pysamerr, "Option: -s simple (yet incomplete) pileup format\n");
- fprintf(pysamerr, " -S the input is in SAM\n");
- fprintf(pysamerr, " -B disable BAQ computation\n");
- fprintf(pysamerr, " -A use the original MAQ model for SNP calling (DEPRECATED)\n");
- fprintf(pysamerr, " -2 output the 2nd best call and quality\n");
- fprintf(pysamerr, " -i only show lines/consensus with indels\n");
- fprintf(pysamerr, " -Q INT min base quality (possibly capped by BAQ) [%d]\n", d->c->min_baseQ);
- fprintf(pysamerr, " -C INT coefficient for adjusting mapQ of poor mappings [%d]\n", d->capQ_thres);
- fprintf(pysamerr, " -m INT filtering reads with bits in INT [0x%x]\n", d->mask);
- fprintf(pysamerr, " -M INT cap mapping quality at INT [%d]\n", d->c->cap_mapQ);
- fprintf(pysamerr, " -d INT limit maximum depth for indels [%d]\n", d->max_depth);
- fprintf(pysamerr, " -t FILE list of reference sequences (force -S)\n");
- fprintf(pysamerr, " -l FILE list of sites at which pileup is output\n");
- fprintf(pysamerr, " -f FILE reference sequence in the FASTA format\n\n");
- fprintf(pysamerr, " -c compute the consensus sequence\n");
- fprintf(pysamerr, " -v print variants only (for -c)\n");
- fprintf(pysamerr, " -g output in the GLFv3 format (DEPRECATED)\n");
- fprintf(pysamerr, " -T FLOAT theta in maq consensus calling model (for -c) [%.4g]\n", d->c->theta);
- fprintf(pysamerr, " -N INT number of haplotypes in the sample (for -c) [%d]\n", d->c->n_hap);
- fprintf(pysamerr, " -r FLOAT prior of a difference between two haplotypes (for -c) [%.4g]\n", d->c->het_rate);
- fprintf(pysamerr, " -G FLOAT prior of an indel between two haplotypes (for -c) [%.4g]\n", d->ido->r_indel);
- fprintf(pysamerr, " -I INT phred prob. of an indel in sequencing/prep. (for -c) [%d]\n", d->ido->q_indel);
- fprintf(pysamerr, "\n");
- fprintf(pysamerr, "Warning: Please use the `mpileup' command instead `pileup'. `Pileup' is deprecated!\n\n");
- free(fn_list); free(fn_fa); free(d);
- return 1;
- }
- if (d->format & (BAM_PLF_RANBASE|BAM_PLF_1STBASE|BAM_PLF_ALLBASE)) d->format |= BAM_PLF_CNS;
- if (fn_fa) d->fai = fai_load(fn_fa);
- if (d->format & (BAM_PLF_CNS|BAM_PLF_GLF)) bam_maqcns_prepare(d->c); // consensus calling
- if (d->format & BAM_PLF_GLF) { // for glf output
- glf3_header_t *h;
- h = glf3_header_init();
- d->fp_glf = bgzf_fdopen(fileno(stdout), "w");
- glf3_header_write(d->fp_glf, h);
- glf3_header_destroy(h);
- }
- if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)))
- fprintf(pysamerr, "[bam_pileup] indels will not be called when -f is absent.\n");
- if (fn_fa && is_SAM && fn_list == 0) fn_list = samfaipath(fn_fa);
-
- {
- samfile_t *fp;
- fp = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);
- if (fp == 0 || fp->header == 0) {
- fprintf(pysamerr, "[bam_pileup] fail to read the header: non-exisiting file or wrong format.\n");
- return 1;
- }
- d->h = fp->header;
- if (fn_pos) d->hash = load_pos(fn_pos, d->h);
- { // run pileup
- extern int bam_prob_realn(bam1_t *b, const char *ref);
- extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
- bam1_t *b;
- int ret, tid, pos, n_plp;
- bam_plp_t iter;
- const bam_pileup1_t *plp;
- b = bam_init1();
- iter = bam_plp_init(0, 0);
- bam_plp_set_mask(iter, d->mask);
- while ((ret = samread(fp, b)) >= 0) {
- int skip = 0;
- if ((int)b->core.tid < 0) break;
- // update d->ref if necessary
- if (d->fai && (int)b->core.tid != d->tid) {
- free(d->ref);
- d->ref = faidx_fetch_seq(d->fai, d->h->target_name[b->core.tid], 0, 0x7fffffff, &d->len);
- d->tid = b->core.tid;
- }
- if (d->ref && (d->format&BAM_PLF_CNS) && !(d->format&BAM_PLF_NOBAQ)) bam_prob_realn(b, d->ref);
- if (d->ref && (d->format&BAM_PLF_CNS) && d->capQ_thres > 10) {
- int q = bam_cap_mapQ(b, d->ref, d->capQ_thres);
- if (q < 0) skip = 1;
- else if (b->core.qual > q) b->core.qual = q;
- } else if (b->core.flag&BAM_FUNMAP) skip = 1;
- else if ((d->format&BAM_PLF_CNS) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1;
- if (skip) continue;
- bam_plp_push(iter, b);
- while ((plp = bam_plp_next(iter, &tid, &pos, &n_plp)) != 0)
- pileup_func(tid, pos, n_plp, plp, d);
- }
- bam_plp_push(iter, 0);
- while ((plp = bam_plp_next(iter, &tid, &pos, &n_plp)) != 0)
- pileup_func(tid, pos, n_plp, plp, d);
- bam_plp_destroy(iter);
- bam_destroy1(b);
- }
- samclose(fp); // d->h will be destroyed here
- }
-
- // free
- if (d->format & BAM_PLF_GLF) bgzf_close(d->fp_glf);
- if (fn_pos) { // free the hash table
- khint_t k;
- for (k = kh_begin(d->hash); k < kh_end(d->hash); ++k)
- if (kh_exist(d->hash, k)) free(kh_val(d->hash, k));
- kh_destroy(64, d->hash);
- }
- free(fn_pos); free(fn_list); free(fn_fa);
- if (d->fai) fai_destroy(d->fai);
- bam_maqcns_destroy(d->c);
- free(d->ido); free(d->ref); free(d);
- return 0;
-}
-
-/***********
- * mpileup *
- ***********/
-
#include <assert.h>
#include "bam2bcf.h"
#include "sample.h"
#define MPLP_NO_INDEL 0x400
#define MPLP_EXT_BAQ 0x800
#define MPLP_ILLUMINA13 0x1000
+#define MPLP_IGNORE_RG 0x2000
+#define MPLP_PRINT_POS 0x4000
+#define MPLP_PRINT_MAPQ 0x8000
void *bed_read(const char *fn);
void bed_destroy(void *_h);
}
static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
- int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp)
+ int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg)
{
int i, j;
memset(m->n_plp, 0, m->n * sizeof(int));
const bam_pileup1_t *p = plp[i] + j;
uint8_t *q;
int id = -1;
- q = bam_aux_get(p->b, "RG");
+ q = ignore_rg? 0 : bam_aux_get(p->b, "RG");
if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf);
if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf);
if (id < 0 || id >= m->n) {
extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
extern void bcf_call_del_rghash(void *rghash);
mplp_aux_t **data;
- int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid, max_depth, max_indel_depth;
+ int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth;
const bam_pileup1_t **plp;
bam_mplp_t iter;
bam_header_t *h = 0;
data[i]->conf = conf;
h_tmp = bam_header_read(data[i]->fp);
data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
- bam_smpl_add(sm, fn[i], h_tmp->text);
+ bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
if (conf->reg) {
int beg, end;
fprintf(pysamerr, "[%s] malformatted region or wrong seqname for %d-th input.\n", __func__, i+1);
exit(1);
}
- if (i == 0) beg0 = beg, end0 = end;
+ if (i == 0) tid0 = tid, beg0 = beg, end0 = end;
data[i]->iter = bam_iter_query(idx, tid, beg, end);
bam_index_destroy(idx);
}
bca->min_frac = conf->min_frac;
bca->min_support = conf->min_support;
}
- ref_tid = -1; ref = 0;
+ if (tid0 >= 0 && conf->fai) { // region is set
+ ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
+ ref_tid = tid0;
+ for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0;
+ } else ref_tid = -1, ref = 0;
iter = bam_mplp_init(n, mplp_func, (void**)data);
max_depth = conf->max_depth;
if (max_depth * sm->n > 1<<20)
if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
if (tid != ref_tid) {
free(ref); ref = 0;
- if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
+ if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len);
for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid;
ref_tid = tid;
}
int total_depth, _ref0, ref16;
bcf1_t *b = calloc(1, sizeof(bcf1_t));
for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
- group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp);
+ group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG);
_ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
ref16 = bam_nt16_table[_ref0];
for (i = 0; i < gplp.n; ++i)
for (i = 0; i < n; ++i) {
int j;
printf("\t%d\t", n_plp[i]);
- if (n_plp[i] == 0) printf("*\t*");
- else {
+ if (n_plp[i] == 0) {
+ printf("*\t*"); // FIXME: printf() is very slow...
+ if (conf->flag & MPLP_PRINT_POS) printf("\t*");
+ } else {
for (j = 0; j < n_plp[i]; ++j)
pileup_seq(plp[i] + j, pos, ref_len, ref);
putchar('\t');
if (c > 126) c = 126;
putchar(c);
}
+ if (conf->flag & MPLP_PRINT_MAPQ) {
+ putchar('\t');
+ for (j = 0; j < n_plp[i]; ++j) {
+ int c = plp[i][j].b->core.qual + 33;
+ if (c > 126) c = 126;
+ putchar(c);
+ }
+ }
+ if (conf->flag & MPLP_PRINT_POS) {
+ putchar('\t');
+ for (j = 0; j < n_plp[i]; ++j) {
+ if (j > 0) putchar(',');
+ printf("%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow...
+ }
+ }
}
}
putchar('\n');
int nfiles = 0, use_orphan = 0;
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
+ #define MPLP_PRINT_POS 0x4000
mplp.max_mq = 60;
mplp.min_baseQ = 13;
mplp.capQ_thres = 0;
mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
mplp.min_frac = 0.002; mplp.min_support = 1;
mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
- while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6")) >= 0) {
+ while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6Os")) >= 0) {
switch (c) {
case 'f':
mplp.fai = fai_load(optarg);
case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
case 'B': mplp.flag &= ~MPLP_REALN; break;
- case 'R': mplp.flag |= MPLP_REALN; break;
case 'D': mplp.flag |= MPLP_FMT_DP; break;
case 'S': mplp.flag |= MPLP_FMT_SP; break;
case 'I': mplp.flag |= MPLP_NO_INDEL; break;
case 'E': mplp.flag |= MPLP_EXT_BAQ; break;
case '6': mplp.flag |= MPLP_ILLUMINA13; break;
+ case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
+ case 's': mplp.flag |= MPLP_PRINT_MAPQ; break;
+ case 'O': mplp.flag |= MPLP_PRINT_POS; break;
case 'C': mplp.capQ_thres = atoi(optarg); break;
case 'M': mplp.max_mq = atoi(optarg); break;
case 'q': mplp.min_mq = atoi(optarg); break;
fprintf(pysamerr, " -A count anomalous read pairs\n");
fprintf(pysamerr, " -B disable BAQ computation\n");
fprintf(pysamerr, " -b FILE list of input BAM files [null]\n");
+ fprintf(pysamerr, " -C INT parameter for adjusting mapQ; 0 to disable [0]\n");
fprintf(pysamerr, " -d INT max per-BAM depth to avoid excessive memory usage [%d]\n", mplp.max_depth);
fprintf(pysamerr, " -E extended BAQ for higher sensitivity but lower specificity\n");
fprintf(pysamerr, " -f FILE faidx indexed reference sequence file [null]\n");
fprintf(pysamerr, " -l FILE list of positions (chr pos) or regions (BED) [null]\n");
fprintf(pysamerr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
fprintf(pysamerr, " -r STR region in which pileup is generated [null]\n");
+ fprintf(pysamerr, " -R ignore RG tags\n");
fprintf(pysamerr, " -q INT skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq);
fprintf(pysamerr, " -Q INT skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ);
fprintf(pysamerr, "\nOutput options:\n\n");
fprintf(pysamerr, " -D output per-sample DP in BCF (require -g/-u)\n");
fprintf(pysamerr, " -g generate BCF output (genotype likelihoods)\n");
+ fprintf(pysamerr, " -O output base positions on reads (disabled by -g/-u)\n");
+ fprintf(pysamerr, " -s output mapping quality (disabled by -g/-u)\n");
fprintf(pysamerr, " -S output per-sample strand bias P-value in BCF (require -g/-u)\n");
fprintf(pysamerr, " -u generate uncompress BCF output\n");
fprintf(pysamerr, "\nSNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):\n\n");
--- /dev/null
+#include "pysam.h"
+
+#include <stdio.h>
+#include <stdlib.h>
+#include "bgzf.h"
+#include "bam.h"
+
+#define BUF_SIZE 0x10000
+
+int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
+{
+ BGZF *fp;
+ bam_header_t *old;
+ int len;
+ uint8_t *buf;
+ if (in->open_mode != 'r') return -1;
+ buf = malloc(BUF_SIZE);
+ old = bam_header_read(in);
+ fp = bgzf_fdopen(fd, "w");
+ bam_header_write(fp, h);
+ if (in->block_offset < in->block_length) {
+ bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
+ bgzf_flush(fp);
+ }
+#ifdef _USE_KNETFILE
+ while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0)
+ fwrite(buf, 1, len, fp->x.fpw);
+#else
+ while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
+ fwrite(buf, 1, len, fp->file);
+#endif
+ free(buf);
+ fp->block_offset = in->block_offset = 0;
+ bgzf_close(fp);
+ return 0;
+}
+
+int main_reheader(int argc, char *argv[])
+{
+ bam_header_t *h;
+ BGZF *in;
+ if (argc != 3) {
+ fprintf(pysamerr, "Usage: samtools reheader <in.header.sam> <in.bam>\n");
+ return 1;
+ }
+ { // read the header
+ tamFile fph = sam_open(argv[1]);
+ if (fph == 0) {
+ fprintf(pysamerr, "[%s] fail to read the header from %s.\n", __func__, argv[1]);
+ return 1;
+ }
+ h = sam_header_read(fph);
+ sam_close(fph);
+ }
+ in = strcmp(argv[2], "-")? bam_open(argv[2], "r") : bam_dopen(fileno(stdin), "r");
+ if (in == 0) {
+ fprintf(pysamerr, "[%s] fail to open file %s.\n", __func__, argv[2]);
+ return 1;
+ }
+ bam_reheader(in, h, fileno(stdout));
+ bgzf_close(in);
+ return 0;
+}
#include <ctype.h>
#include <assert.h>
#include <string.h>
+#include <math.h>
#include "bam.h"
#include "faidx.h"
-#include "bam_maqcns.h"
+#include "bam2bcf.h"
char bam_aux_getCEi(bam1_t *b, int i);
char bam_aux_getCSi(bam1_t *b, int i);
bamFile fp;
int curr_tid, left_pos;
faidx_t *fai;
- bam_maqcns_t *bmc;
+ bcf_callaux_t *bca;
int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;
char *ref;
int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
{
+ extern unsigned char bam_nt16_table[256];
tview_t *tv = (tview_t*)data;
int i, j, c, rb, attr, max_ins = 0;
uint32_t call = 0;
mvaddch(1, tv->ccol++, c);
}
if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
- // print consensus
- call = bam_maqcns_call(n, pl, tv->bmc);
+ { // call consensus
+ bcf_callret1_t bcr;
+ int qsum[4], a1, a2, tmp;
+ double p[3], prior = 30;
+ bcf_call_glfgen(n, pl, bam_nt16_table[rb], tv->bca, &bcr);
+ for (i = 0; i < 4; ++i) qsum[i] = bcr.qsum[i]<<2 | i;
+ for (i = 1; i < 4; ++i) // insertion sort
+ for (j = i; j > 0 && qsum[j] > qsum[j-1]; --j)
+ tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
+ a1 = qsum[0]&3; a2 = qsum[1]&3;
+ p[0] = bcr.p[a1*5+a1]; p[1] = bcr.p[a1*5+a2] + prior; p[2] = bcr.p[a2*5+a2];
+ if ("ACGT"[a1] != toupper(rb)) p[0] += prior + 3;
+ if ("ACGT"[a2] != toupper(rb)) p[2] += prior + 3;
+ if (p[0] < p[1] && p[0] < p[2]) call = (1<<a1)<<16 | (int)((p[1]<p[2]?p[1]:p[2]) - p[0] + .499);
+ else if (p[2] < p[1] && p[2] < p[0]) call = (1<<a2)<<16 | (int)((p[0]<p[1]?p[0]:p[1]) - p[2] + .499);
+ else call = (1<<a1|1<<a2)<<16 | (int)((p[0]<p[2]?p[0]:p[2]) - p[1] + .499);
+ }
attr = A_UNDERLINE;
- c = ",ACMGRSVTWYHKDBN"[call>>28&0xf];
- i = (call>>8&0xff)/10+1;
+ c = ",ACMGRSVTWYHKDBN"[call>>16&0xf];
+ i = (call&0xffff)/10+1;
if (i > 4) i = 4;
attr |= COLOR_PAIR(i);
if (c == toupper(rb)) c = '.';
if (tv->idx == 0) exit(1);
tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
if (fn_fa) tv->fai = fai_load(fn_fa);
- tv->bmc = bam_maqcns_init();
+ tv->bca = bcf_call_init(0.83, 13);
tv->ins = 1;
- bam_maqcns_prepare(tv->bmc);
initscr();
keypad(stdscr, TRUE);
endwin();
bam_lplbuf_destroy(tv->lplbuf);
- bam_maqcns_destroy(tv->bmc);
+ bcf_call_destroy(tv->bca);
bam_index_destroy(tv->idx);
if (tv->fai) fai_destroy(tv->fai);
free(tv->ref);
#ifndef BCF_H
#define BCF_H
+#define BCF_VERSION "0.1.17-dev (r973:277)"
+
#include <stdint.h>
#include <zlib.h>
int bcf_fix_gt(bcf1_t *b);
// update PL generated by old samtools
int bcf_fix_pl(bcf1_t *b);
+ // convert PL to GLF-like 10-likelihood GL
+ int bcf_gl10(const bcf1_t *b, uint8_t *gl);
+ // convert up to 4 INDEL alleles to GLF-like 10-likelihood GL
+ int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl);
// string hash table
void *bcf_build_refhash(bcf_hdr_t *h);
#include "khash.h"
KHASH_MAP_INIT_STR(str2id, int)
+#ifdef _WIN32
+#define srand48(x) srand(x)
+#define drand48() ((double)rand() / RAND_MAX)
+#endif
+
+// FIXME: valgrind report a memory leak in this function. Probably it does not get deallocated...
void *bcf_build_refhash(bcf_hdr_t *h)
{
khash_t(str2id) *hash;
b->n_smpl = n_smpl;
return 0;
}
+
+static int8_t nt4_table[128] = {
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 /*'-'*/, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 3, 4, 4, 4, -1, 4, 4, 4, 4, 4, 4, 4,
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 3, 4, 4, 4, -1, 4, 4, 4, 4, 4, 4, 4
+};
+
+int bcf_gl10(const bcf1_t *b, uint8_t *gl)
+{
+ int a[4], k, l, map[4], k1, j, i;
+ const bcf_ginfo_t *PL;
+ char *s;
+ if (b->ref[1] != 0 || b->n_alleles > 4) return -1; // ref is not a single base or >4 alleles
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+ if (i == b->n_gi) return -1; // no PL
+ PL = b->gi + i;
+ a[0] = nt4_table[(int)b->ref[0]];
+ if (a[0] > 3 || a[0] < 0) return -1; // ref is not A/C/G/T
+ a[1] = a[2] = a[3] = -2; // -1 has a special meaning
+ if (b->alt[0] == 0) return -1; // no alternate allele
+ map[0] = map[1] = map[2] = map[3] = -2;
+ map[a[0]] = 0;
+ for (k = 0, s = b->alt, k1 = -1; k < 3 && *s; ++k, s += 2) {
+ if (s[1] != ',' && s[1] != 0) return -1; // ALT is not single base
+ a[k+1] = nt4_table[(int)*s];
+ if (a[k+1] >= 0) map[a[k+1]] = k+1;
+ else k1 = k + 1;
+ if (s[1] == 0) break; // the end of the ALT string
+ }
+ for (k = 0; k < 4; ++k)
+ if (map[k] < 0) map[k] = k1;
+ for (i = 0; i < b->n_smpl; ++i) {
+ const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
+ uint8_t *g = gl + 10 * i;
+ for (k = j = 0; k < 4; ++k) {
+ for (l = k; l < 4; ++l) {
+ int t, x = map[k], y = map[l];
+ if (x > y) t = x, x = y, y = t; // make sure x is the smaller
+ g[j++] = p[y * (y+1) / 2 + x];
+ }
+ }
+ }
+ return 0;
+}
+
+int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl)
+{
+ int k, l, j, i;
+ const bcf_ginfo_t *PL;
+ if (b->alt[0] == 0) return -1; // no alternate allele
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+ if (i == b->n_gi) return -1; // no PL
+ PL = b->gi + i;
+ for (i = 0; i < b->n_smpl; ++i) {
+ const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
+ uint8_t *g = gl + 10 * i;
+ for (k = j = 0; k < 4; ++k) {
+ for (l = k; l < 4; ++l) {
+ int t, x = k, y = l;
+ if (x > y) t = x, x = y, y = t; // make sure x is the smaller
+ x = y * (y+1) / 2 + x;
+ g[j++] = x < PL->len? p[x] : 255;
+ }
+ }
+ }
+ return 0;
+}
#include "kstring.h"
#include "time.h"
+#ifdef _WIN32
+#define srand48(x) srand(x)
+#define lrand48() rand()
+#endif
+
#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 16384)
#define VC_ANNO_MAX 16384
#define VC_FIX_PL 32768
#define VC_EM 0x10000
+#define VC_PAIRCALL 0x20000
+#define VC_QCNT 0x40000
typedef struct {
int flag, prior_type, n1, n_sub, *sublist, n_perm;
+ uint32_t *trio_aux;
char *prior_file, **subsam, *fn_dict;
uint8_t *ploidy;
double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt;
bcf_sync(b);
}
-static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[9])
+static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[10], int cons_llr, int64_t cons_gt)
{
kstring_t s;
int has_I16, is_var;
if (em[4] >= 0 && em[4] <= 0.05) ksprintf(&s, ";G3=%.4g,%.4g,%.4g;HWE=%.3g", em[3], em[2], em[1], em[4]);
if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
+ if (em[8] >= 0) ksprintf(&s, ";LRT2=%.3g", em[8]);
+ }
+ if (cons_llr > 0) {
+ ksprintf(&s, ";CLR=%d", cons_llr);
+ if (cons_gt > 0)
+ ksprintf(&s, ";UGT=%c%c%c;CGT=%c%c%c", cons_gt&0xff, cons_gt>>8&0xff, cons_gt>>16&0xff,
+ cons_gt>>32&0xff, cons_gt>>40&0xff, cons_gt>>48&0xff);
}
if (pr == 0) { // if pr is unset, return
kputc('\0', &s); kputs(b->fmt, &s); kputc('\0', &s);
is_var = (pr->p_ref < pref);
r = is_var? pr->p_ref : pr->p_var;
- ksprintf(&s, ";CI95=%.4g,%.4g", pr->cil, pr->cih); // FIXME: when EM is not used, ";" should be omitted!
+// ksprintf(&s, ";CI95=%.4g,%.4g", pr->cil, pr->cih); // FIXME: when EM is not used, ";" should be omitted!
+ ksprintf(&s, ";AC1=%d", pr->ac);
if (has_I16) ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded);
if (fq < -999) fq = -999;
if (q[i] > 255) q[i] = 255;
}
if (pr->perm_rank >= 0) ksprintf(&s, ";PR=%d", pr->perm_rank);
+ // ksprintf(&s, ";LRT3=%.3g", pr->lrt);
ksprintf(&s, ";PCHI2=%.3g;PC2=%d,%d", q[1], q[2], pr->p_chi2);
}
if (has_I16 && a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
if (!strstr(str.s, "##INFO=<ID=FQ,"))
kputs("##INFO=<ID=FQ,Number=1,Type=Float,Description=\"Phred probability of all samples being the same\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=AF1,"))
- kputs("##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the site allele frequency of the first ALT allele\">\n", &str);
+ kputs("##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele frequency (assuming HWE)\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=AC1,"))
+ kputs("##INFO=<ID=AC1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele count (no HWE assumption)\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=G3,"))
kputs("##INFO=<ID=G3,Number=3,Type=Float,Description=\"ML estimate of genotype frequencies\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=HWE,"))
kputs("##INFO=<ID=HWE,Number=1,Type=Float,Description=\"Chi^2 based HWE test P-value based on G3\">\n", &str);
- if (!strstr(str.s, "##INFO=<ID=CI95,"))
- kputs("##INFO=<ID=CI95,Number=2,Type=Float,Description=\"Equal-tail Bayesian credible interval of the site allele frequency at the 95% level\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=CLR,"))
+ kputs("##INFO=<ID=CLR,Number=1,Type=Integer,Description=\"Log ratio of genotype likelihoods with and without the constraint\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=UGT,"))
+ kputs("##INFO=<ID=UGT,Number=1,Type=String,Description=\"The most probable unconstrained genotype configuration in the trio\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=CGT,"))
+ kputs("##INFO=<ID=CGT,Number=1,Type=String,Description=\"The most probable constrained genotype configuration in the trio\">\n", &str);
+// if (!strstr(str.s, "##INFO=<ID=CI95,"))
+// kputs("##INFO=<ID=CI95,Number=2,Type=Float,Description=\"Equal-tail Bayesian credible interval of the site allele frequency at the 95% level\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=PV4,"))
kputs("##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=INDEL,"))
kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=RP,"))
kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=VDB,"))
+ kputs("##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=GT,"))
kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
if (!strstr(str.s, "##FORMAT=<ID=SP,"))
kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=PL,"))
- kputs("##FORMAT=<ID=PL,Number=-1,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2\">\n", &str);
+ kputs("##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">\n", &str);
h->l_txt = str.l + 1; h->txt = str.s;
}
extern int bcf_fix_gt(bcf1_t *b);
extern int bcf_anno_max(bcf1_t *b);
extern int bcf_shuffle(bcf1_t *b, int seed);
+ extern uint32_t *bcf_trio_prep(int is_x, int is_son);
+ extern int bcf_trio_call(uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt);
+ extern int bcf_pair_call(const bcf1_t *b);
+ extern int bcf_min_diff(const bcf1_t *b);
+
bcf_t *bp, *bout = 0;
bcf1_t *b, *blast;
int c, *seeds = 0;
- uint64_t n_processed = 0;
+ uint64_t n_processed = 0, qcnt[256];
viewconf_t vc;
bcf_p1aux_t *p1 = 0;
bcf_hdr_t *hin, *hout;
tid = begin = end = -1;
memset(&vc, 0, sizeof(viewconf_t));
vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1;
- while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:")) >= 0) {
+ memset(qcnt, 0, 8 * 256);
+ while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Y")) >= 0) {
switch (c) {
case '1': vc.n1 = atoi(optarg); break;
case 'l': vc.bed = bed_read(optarg); break;
case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
case 'I': vc.flag |= VC_NO_INDEL; break;
case 'M': vc.flag |= VC_ANNO_MAX; break;
+ case 'Y': vc.flag |= VC_QCNT; break;
case 't': vc.theta = atof(optarg); break;
case 'p': vc.pref = atof(optarg); break;
case 'i': vc.indel_frac = atof(optarg); break;
for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
tid = -1;
break;
+ case 'T':
+ if (strcmp(optarg, "trioauto") == 0) vc.trio_aux = bcf_trio_prep(0, 0);
+ else if (strcmp(optarg, "trioxd") == 0) vc.trio_aux = bcf_trio_prep(1, 0);
+ else if (strcmp(optarg, "trioxs") == 0) vc.trio_aux = bcf_trio_prep(1, 1);
+ else if (strcmp(optarg, "pair") == 0) vc.flag |= VC_PAIRCALL;
+ else {
+ fprintf(pysamerr, "[%s] Option '-T' can only take value trioauto, trioxd or trioxs.\n", __func__);
+ return 1;
+ }
+ break;
case 'P':
if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL;
else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2;
fprintf(pysamerr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
fprintf(pysamerr, " -P STR type of prior: full, cond2, flat [full]\n");
fprintf(pysamerr, " -t FLOAT scaled substitution mutation rate [%.4g]\n", vc.theta);
+ fprintf(pysamerr, " -T STR constrained calling; STR can be: pair, trioauto, trioxd and trioxs (see manual) [null]\n");
fprintf(pysamerr, " -v output potential variant sites only (force -c)\n");
fprintf(pysamerr, "\nContrast calling and association test options:\n\n");
fprintf(pysamerr, " -1 INT number of group-1 samples [0]\n");
}
}
while (vcf_read(bp, hin, b) > 0) {
- int is_indel;
- double em[9];
+ int is_indel, cons_llr = -1;
+ int64_t cons_gt = -1;
+ double em[10];
if ((vc.flag & VC_VARONLY) && strcmp(b->alt, "X") == 0) continue;
if ((vc.flag & VC_VARONLY) && vc.min_smpl_frac > 0.) {
extern int bcf_smpl_covered(const bcf1_t *b);
if (!(l > begin && end > b->pos)) continue;
}
++n_processed;
+ if ((vc.flag & VC_QCNT) && !is_indel) { // summarize the difference
+ int x = bcf_min_diff(b);
+ if (x > 255) x = 255;
+ if (x >= 0) ++qcnt[x];
+ }
if (vc.flag & VC_QCALL) { // output QCALL format; STOP here
bcf_2qcall(hout, b);
continue;
}
- if (vc.flag & VC_EM) bcf_em1(b, vc.n1, 0xff, em);
+ if (vc.trio_aux) // do trio calling
+ bcf_trio_call(vc.trio_aux, b, &cons_llr, &cons_gt);
+ else if (vc.flag & VC_PAIRCALL)
+ cons_llr = bcf_pair_call(b);
+ if (vc.flag & (VC_CALL|VC_ADJLD|VC_EM)) bcf_gl2pl(b);
+ if (vc.flag & VC_EM) bcf_em1(b, vc.n1, 0x1ff, em);
else {
int i;
for (i = 0; i < 9; ++i) em[i] = -1.;
}
- if (vc.flag & (VC_CALL|VC_ADJLD)) bcf_gl2pl(b);
if (vc.flag & VC_CALL) { // call variants
bcf_p1rst_t pr;
int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
int i, n = 0;
for (i = 0; i < vc.n_perm; ++i) {
#ifdef BCF_PERM_LRT // LRT based permutation is much faster but less robust to artifacts
- double x[9];
+ double x[10];
bcf_shuffle(b, seeds[i]);
bcf_em1(b, vc.n1, 1<<7, x);
if (x[7] < em[7]) ++n;
}
pr.perm_rank = n;
}
- if (calret >= 0) update_bcf1(b, p1, &pr, vc.pref, vc.flag, em);
- } else if (vc.flag & VC_EM) update_bcf1(b, 0, 0, 0, vc.flag, em);
+ if (calret >= 0) update_bcf1(b, p1, &pr, vc.pref, vc.flag, em, cons_llr, cons_gt);
+ } else if (vc.flag & VC_EM) update_bcf1(b, 0, 0, 0, vc.flag, em, cons_llr, cons_gt);
if (vc.flag & VC_ADJLD) { // compute LD
double f[4], r2;
if ((r2 = bcf_pair_freq(blast, b, f)) >= 0) {
vcf_close(bp); vcf_close(bout);
if (vc.fn_dict) free(vc.fn_dict);
if (vc.ploidy) free(vc.ploidy);
+ if (vc.trio_aux) free(vc.trio_aux);
if (vc.n_sub) {
int i;
for (i = 0; i < vc.n_sub; ++i) free(vc.subsam[i]);
free(vc.subsam); free(vc.sublist);
}
if (vc.bed) bed_destroy(vc.bed);
+ if (vc.flag & VC_QCNT)
+ for (c = 0; c < 256; ++c)
+ fprintf(pysamerr, "QT\t%d\t%lld\n", c, (long long)qcnt[c]);
if (seeds) free(seeds);
if (p1) bcf_p1_destroy(p1);
return 0;
// x[5..6]: group1 freq, group2 freq
// x[7]: 1-degree P-value
// x[8]: 2-degree P-value
-int bcf_em1(const bcf1_t *b, int n1, int flag, double x[9])
+int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10])
{
double *pdg;
int i, n, n2;
n = b->n_smpl; n2 = n - n1;
pdg = get_pdg3(b);
if (pdg == 0) return -1;
- for (i = 0; i < 9; ++i) x[i] = -1.;
+ for (i = 0; i < 10; ++i) x[i] = -1.; // set to negative
{
if ((x[0] = est_freq(n, pdg)) < 0.) {
free(pdg);
}
x[0] = freqml(x[0], 0, n, pdg);
}
- if (flag & (0xf<<1|1<<8)) { // estimate the genotype frequency and test HWE
+ if (flag & (0xf<<1|3<<8)) { // estimate the genotype frequency and test HWE
double *g = x + 1, f3[3], r;
f3[0] = g[0] = (1 - x[0]) * (1 - x[0]);
f3[1] = g[1] = 2 * x[0] * (1 - x[0]);
x[6] = freqml(x[0], n1, n, pdg);
}
if ((flag & 1<<7) && n1 > 0 && n1 < n) { // 1-degree P-value
- double f[3], f3[3][3];
+ double f[3], f3[3][3], tmp;
f[0] = x[0]; f[1] = x[5]; f[2] = x[6];
for (i = 0; i < 3; ++i)
f3[i][0] = (1-f[i])*(1-f[i]), f3[i][1] = 2*f[i]*(1-f[i]), f3[i][2] = f[i]*f[i];
- x[7] = kf_gammaq(.5, log(lk_ratio_test(n, n1, pdg, f3)));
+ tmp = log(lk_ratio_test(n, n1, pdg, f3));
+ if (tmp < 0) tmp = 0;
+ x[7] = kf_gammaq(.5, tmp);
}
- if ((flag & 1<<8) && n1 > 0 && n1 < n) { // 2-degree P-value
- double g[3][3];
+ if ((flag & 3<<8) && n1 > 0 && n1 < n) { // 2-degree P-value
+ double g[3][3], tmp;
for (i = 0; i < 3; ++i) memcpy(g[i], x + 1, 3 * sizeof(double));
for (i = 0; i < ITER_MAX; ++i)
if (g3_iter(g[1], pdg, 0, n1) < EPS) break;
for (i = 0; i < ITER_MAX; ++i)
if (g3_iter(g[2], pdg, n1, n) < EPS) break;
- x[8] = kf_gammaq(1., log(lk_ratio_test(n, n1, pdg, g)));
+ tmp = log(lk_ratio_test(n, n1, pdg, g));
+ if (tmp < 0) tmp = 0;
+ x[8] = kf_gammaq(1., tmp);
}
// free
free(pdg);
--- /dev/null
+#include "pysam.h"
+
+#include <stdlib.h>
+#include <stdint.h>
+#include "bcf.h"
+
+#define MAX_GENO 359
+
+int8_t seq_bitcnt[] = { 4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 };
+char *seq_nt16rev = "XACMGRSVTWYHKDBN";
+
+uint32_t *bcf_trio_prep(int is_x, int is_son)
+{
+ int i, j, k, n, map[10];
+ uint32_t *ret;
+ ret = calloc(MAX_GENO, 4);
+ for (i = 0, k = 0; i < 4; ++i)
+ for (j = i; j < 4; ++j)
+ map[k++] = 1<<i|1<<j;
+ for (i = 0, n = 1; i < 10; ++i) { // father
+ if (is_x && seq_bitcnt[map[i]] != 1) continue;
+ if (is_x && is_son) {
+ for (j = 0; j < 10; ++j) // mother
+ for (k = 0; k < 10; ++k) // child
+ if (seq_bitcnt[map[k]] == 1 && (map[j]&map[k]))
+ ret[n++] = j<<16 | i<<8 | k;
+ } else {
+ for (j = 0; j < 10; ++j) // mother
+ for (k = 0; k < 10; ++k) // child
+ if ((map[i]&map[k]) && (map[j]&map[k]) && ((map[i]|map[j])&map[k]) == map[k])
+ ret[n++] = j<<16 | i<<8 | k;
+ }
+ }
+ ret[0] = n - 1;
+ return ret;
+}
+
+
+int bcf_trio_call(const uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt)
+{
+ int i, j, k;
+ const bcf_ginfo_t *PL;
+ uint8_t *gl10;
+ int map[10];
+ if (b->n_smpl != 3) return -1; // not a trio
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+ if (i == b->n_gi) return -1; // no PL
+ gl10 = alloca(10 * b->n_smpl);
+ if (bcf_gl10(b, gl10) < 0) {
+ if (bcf_gl10_indel(b, gl10) < 0) return -1;
+ }
+ PL = b->gi + i;
+ for (i = 0, k = 0; i < 4; ++i)
+ for (j = i; j < 4; ++j)
+ map[k++] = seq_nt16rev[1<<i|1<<j];
+ for (j = 0; j < 3; ++j) // check if ref hom is the most probable in all members
+ if (((uint8_t*)PL->data)[j * PL->len] != 0) break;
+ if (j < 3) { // we need to go through the complex procedure
+ uint8_t *g[3];
+ int minc = 1<<30, minc_j = -1, minf = 0, gtf = 0, gtc = 0;
+ g[0] = gl10;
+ g[1] = gl10 + 10;
+ g[2] = gl10 + 20;
+ for (j = 1; j <= (int)prep[0]; ++j) { // compute LK with constraint
+ int sum = g[0][prep[j]&0xff] + g[1][prep[j]>>8&0xff] + g[2][prep[j]>>16&0xff];
+ if (sum < minc) minc = sum, minc_j = j;
+ }
+ gtc |= map[prep[minc_j]&0xff]; gtc |= map[prep[minc_j]>>8&0xff]<<8; gtc |= map[prep[minc_j]>>16]<<16;
+ for (j = 0; j < 3; ++j) { // compute LK without constraint
+ int min = 1<<30, min_k = -1;
+ for (k = 0; k < 10; ++k)
+ if (g[j][k] < min) min = g[j][k], min_k = k;
+ gtf |= map[min_k]<<(j*8);
+ minf += min;
+ }
+ *llr = minc - minf; *gt = (int64_t)gtc<<32 | gtf;
+ } else *llr = 0, *gt = -1;
+ return 0;
+}
+
+int bcf_pair_call(const bcf1_t *b)
+{
+ int i, j, k;
+ const bcf_ginfo_t *PL;
+ if (b->n_smpl != 2) return -1; // not a pair
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+ if (i == b->n_gi) return -1; // no PL
+ PL = b->gi + i;
+ for (j = 0; j < 2; ++j) // check if ref hom is the most probable in all members
+ if (((uint8_t*)PL->data)[j * PL->len] != 0) break;
+ if (j < 2) { // we need to go through the complex procedure
+ uint8_t *g[2];
+ int minc = 1<<30, minf = 0;
+ g[0] = PL->data;
+ g[1] = (uint8_t*)PL->data + PL->len;
+ for (j = 0; j < PL->len; ++j) // compute LK with constraint
+ minc = minc < g[0][j] + g[1][j]? minc : g[0][j] + g[1][j];
+ for (j = 0; j < 2; ++j) { // compute LK without constraint
+ int min = 1<<30;
+ for (k = 0; k < PL->len; ++k)
+ min = min < g[j][k]? min : g[j][k];
+ minf += min;
+ }
+ return minc - minf;
+ } else return 0;
+}
+
+int bcf_min_diff(const bcf1_t *b)
+{
+ int i, min = 1<<30;
+ const bcf_ginfo_t *PL;
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+ if (i == b->n_gi) return -1; // no PL
+ PL = b->gi + i;
+ for (i = 0; i < b->n_smpl; ++i) {
+ int m1, m2, j;
+ const uint8_t *p = (uint8_t*)PL->data;
+ m1 = m2 = 1<<30;
+ for (j = 0; j < PL->len; ++j) {
+ if ((int)p[j] < m1) m2 = m1, m1 = p[j];
+ else if ((int)p[j] < m2) m2 = p[j];
+ }
+ min = min < m2 - m1? min : m2 - m1;
+ }
+ return min;
+}
for (k = 0, sum = 0.; k < ma->M; ++k)
sum += ma->afs1[k];
rst->p_var = (double)sum;
+ { // compute the allele count
+ double max = -1;
+ rst->ac = -1;
+ for (k = 0; k <= ma->M; ++k)
+ if (max < ma->z[k]) max = ma->z[k], rst->ac = k;
+ rst->ac = ma->M - rst->ac;
+ }
// calculate f_flat and f_em
for (k = 0, sum = 0.; k <= ma->M; ++k)
sum += (long double)ma->z[k];
{ // estimate equal-tail credible interval (95% level)
int l, h;
double p;
- for (i = 0, p = 0.; i < ma->M; ++i)
+ for (i = 0, p = 0.; i <= ma->M; ++i)
if (p + ma->afs1[i] > 0.025) break;
else p += ma->afs1[i];
l = i;
- for (i = ma->M-1, p = 0.; i >= 0; --i)
+ for (i = ma->M, p = 0.; i >= 0; --i)
if (p + ma->afs1[i] > 0.025) break;
else p += ma->afs1[i];
h = i;
rst->cil = (double)(ma->M - h) / ma->M; rst->cih = (double)(ma->M - l) / ma->M;
}
+ if (ma->n1 > 0) { // compute LRT
+ double max0, max1, max2;
+ for (k = 0, max0 = -1; k <= ma->M; ++k)
+ if (max0 < ma->z[k]) max0 = ma->z[k];
+ for (k = 0, max1 = -1; k <= ma->n1 * 2; ++k)
+ if (max1 < ma->z1[k]) max1 = ma->z1[k];
+ for (k = 0, max2 = -1; k <= ma->M - ma->n1 * 2; ++k)
+ if (max2 < ma->z2[k]) max2 = ma->z2[k];
+ rst->lrt = log(max1 * max2 / max0);
+ rst->lrt = rst->lrt < 0? 1 : kf_gammaq(.5, rst->lrt);
+ } else rst->lrt = -1.0;
rst->cmp[0] = rst->cmp[1] = rst->cmp[2] = rst->p_chi2 = -1.0;
if (do_contrast && rst->p_var > 0.5) // skip contrast2() if the locus is a strong non-variant
rst->p_chi2 = contrast2(ma, rst->cmp);
typedef struct {
int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal()
+ int ac; // ML alternative allele count
double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var;
double cil, cih;
- double cmp[3], p_chi2; // used by contrast2()
+ double cmp[3], p_chi2, lrt; // used by contrast2()
} bcf_p1rst_t;
#define MC_PTYPE_FULL 1
int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
void bcf_p1_set_folded(bcf_p1aux_t *p1a); // only effective when set_n1() is not called
- int bcf_em1(const bcf1_t *b, int n1, int flag, double x[9]);
+ int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10]);
#ifdef __cplusplus
}
#include <stdio.h>
#include <zlib.h>
+#ifdef _WIN32
+#define drand48() ((double)rand() / RAND_MAX)
+#endif
+
#include "ksort.h"
KSORT_INIT_GENERIC(uint64_t)
if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
beg = atoi(str->s); // begin
if (dret != '\n') {
- if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0]))
+ if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
end = atoi(str->s); // end
+ if (end < beg) end = -1;
+ }
}
}
}
#include "khash.h"
typedef struct {
- uint64_t len:32, line_len:16, line_blen:16;
+ int32_t line_len, line_blen;
+ int64_t len;
uint64_t offset;
} faidx1_t;
KHASH_MAP_INIT_STR(s, faidx1_t)
{
char c, *name;
int l_name, m_name, ret;
- int len, line_len, line_blen, state;
+ int line_len, line_blen, state;
int l1, l2;
faidx_t *idx;
uint64_t offset;
+ int64_t len;
idx = (faidx_t*)calloc(1, sizeof(faidx_t));
idx->hash = kh_init(s);
return 0;
}
++l1; len += l2;
- if (l2 >= 0x10000) {
- fprintf(pysamerr, "[fai_build_core] line length exceeds 65535 in sequence '%s'.\n", name);
- free(name); fai_destroy(idx);
- return 0;
- }
if (state == 1) line_len = l1, line_blen = l2, state = 0;
else if (state == 0) {
if (l1 != line_len || l2 != line_blen) state = 2;
char *fai_fetch(const faidx_t *fai, const char *str, int *len)
{
- char *s, *p, c;
- int i, l, k;
+ char *s, c;
+ int i, l, k, name_end;
khiter_t iter;
faidx1_t val;
khash_t(s) *h;
beg = end = -1;
h = fai->hash;
- l = strlen(str);
- p = s = (char*)malloc(l+1);
- /* squeeze out "," */
- for (i = k = 0; i != l; ++i)
- if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
- s[k] = 0;
- for (i = 0; i != k; ++i) if (s[i] == ':') break;
- s[i] = 0;
- iter = kh_get(s, h, s); /* get the ref_id */
- if (iter == kh_end(h)) {
- *len = 0;
- free(s); return 0;
- }
+ name_end = l = strlen(str);
+ s = (char*)malloc(l+1);
+ // remove space
+ for (i = k = 0; i < l; ++i)
+ if (!isspace(str[i])) s[k++] = str[i];
+ s[k] = 0; l = k;
+ // determine the sequence name
+ for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
+ if (i >= 0) name_end = i;
+ if (name_end < l) { // check if this is really the end
+ int n_hyphen = 0;
+ for (i = name_end + 1; i < l; ++i) {
+ if (s[i] == '-') ++n_hyphen;
+ else if (!isdigit(s[i]) && s[i] != ',') break;
+ }
+ if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
+ s[name_end] = 0;
+ iter = kh_get(s, h, s);
+ if (iter == kh_end(h)) { // cannot find the sequence name
+ iter = kh_get(s, h, str); // try str as the name
+ if (iter == kh_end(h)) {
+ *len = 0;
+ free(s); return 0;
+ } else s[name_end] = ':', name_end = l;
+ }
+ } else iter = kh_get(s, h, str);
val = kh_value(h, iter);
- if (i == k) { /* dump the whole sequence */
- beg = 0; end = val.len;
- } else {
- for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
- beg = atoi(p);
- if (i < k) {
- p = s + i + 1;
- end = atoi(p);
- } else end = val.len;
- }
- if (beg > 0) --beg;
+ // parse the interval
+ if (name_end < l) {
+ for (i = k = name_end + 1; i < l; ++i)
+ if (s[i] != ',') s[k++] = s[i];
+ s[k] = 0;
+ beg = atoi(s + name_end + 1);
+ for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
+ end = i < k? atoi(s + i + 1) : val.len;
+ if (beg > 0) --beg;
+ } else beg = 0, end = val.len;
if (beg >= val.len) beg = val.len;
if (end >= val.len) end = val.len;
if (beg > end) beg = end;
+++ /dev/null
-#include "pysam.h"
-
-#include <string.h>
-#include <stdlib.h>
-#include "glf.h"
-
-#ifdef _NO_BGZF
-// then alias bgzf_*() functions
-#endif
-
-static int glf3_is_BE = 0;
-
-static inline uint32_t bam_swap_endian_4(uint32_t v)
-{
- v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
- return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
-}
-
-static inline uint16_t bam_swap_endian_2(uint16_t v)
-{
- return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8));
-}
-
-static inline int bam_is_big_endian()
-{
- long one= 1;
- return !(*((char *)(&one)));
-}
-
-glf3_header_t *glf3_header_init()
-{
- glf3_is_BE = bam_is_big_endian();
- return (glf3_header_t*)calloc(1, sizeof(glf3_header_t));
-}
-
-glf3_header_t *glf3_header_read(glfFile fp)
-{
- glf3_header_t *h;
- char magic[4];
- h = glf3_header_init();
- bgzf_read(fp, magic, 4);
- if (strncmp(magic, "GLF\3", 4)) {
- fprintf(pysamerr, "[glf3_header_read] invalid magic.\n");
- glf3_header_destroy(h);
- return 0;
- }
- bgzf_read(fp, &h->l_text, 4);
- if (glf3_is_BE) h->l_text = bam_swap_endian_4(h->l_text);
- if (h->l_text) {
- h->text = (uint8_t*)calloc(h->l_text + 1, 1);
- bgzf_read(fp, h->text, h->l_text);
- }
- return h;
-}
-
-void glf3_header_write(glfFile fp, const glf3_header_t *h)
-{
- int32_t x;
- bgzf_write(fp, "GLF\3", 4);
- x = glf3_is_BE? bam_swap_endian_4(h->l_text) : h->l_text;
- bgzf_write(fp, &x, 4);
- if (h->l_text) bgzf_write(fp, h->text, h->l_text);
-}
-
-void glf3_header_destroy(glf3_header_t *h)
-{
- free(h->text);
- free(h);
-}
-
-char *glf3_ref_read(glfFile fp, int *len)
-{
- int32_t n, x;
- char *str;
- *len = 0;
- if (bgzf_read(fp, &n, 4) != 4) return 0;
- if (glf3_is_BE) n = bam_swap_endian_4(n);
- if (n < 0) {
- fprintf(pysamerr, "[glf3_ref_read] invalid reference name length: %d.\n", n);
- return 0;
- }
- str = (char*)calloc(n + 1, 1); // not necesarily n+1 in fact
- x = bgzf_read(fp, str, n);
- x += bgzf_read(fp, len, 4);
- if (x != n + 4) {
- free(str); *len = -1; return 0; // truncated
- }
- if (glf3_is_BE) *len = bam_swap_endian_4(*len);
- return str;
-}
-
-void glf3_ref_write(glfFile fp, const char *str, int len)
-{
- int32_t m, n = strlen(str) + 1;
- m = glf3_is_BE? bam_swap_endian_4(n) : n;
- bgzf_write(fp, &m, 4);
- bgzf_write(fp, str, n);
- if (glf3_is_BE) len = bam_swap_endian_4(len);
- bgzf_write(fp, &len, 4);
-}
-
-void glf3_view1(const char *ref_name, const glf3_t *g3, int pos)
-{
- int j;
- if (g3->rtype == GLF3_RTYPE_END) return;
- printf("%s\t%d\t%c\t%d\t%d\t%d", ref_name, pos + 1,
- g3->rtype == GLF3_RTYPE_INDEL? '*' : "XACMGRSVTWYHKDBN"[g3->ref_base],
- g3->depth, g3->rms_mapQ, g3->min_lk);
- if (g3->rtype == GLF3_RTYPE_SUB)
- for (j = 0; j != 10; ++j) printf("\t%d", g3->lk[j]);
- else {
- printf("\t%d\t%d\t%d\t%d\t%d\t%s\t%s\t", g3->lk[0], g3->lk[1], g3->lk[2], g3->indel_len[0], g3->indel_len[1],
- g3->indel_len[0]? g3->indel_seq[0] : "*", g3->indel_len[1]? g3->indel_seq[1] : "*");
- }
- printf("\n");
-}
-
-int glf3_write1(glfFile fp, const glf3_t *g3)
-{
- int r;
- uint8_t c;
- uint32_t y[2];
- c = g3->rtype<<4 | g3->ref_base;
- r = bgzf_write(fp, &c, 1);
- if (g3->rtype == GLF3_RTYPE_END) return r;
- y[0] = g3->offset;
- y[1] = g3->min_lk<<24 | g3->depth;
- if (glf3_is_BE) {
- y[0] = bam_swap_endian_4(y[0]);
- y[1] = bam_swap_endian_4(y[1]);
- }
- r += bgzf_write(fp, y, 8);
- r += bgzf_write(fp, &g3->rms_mapQ, 1);
- if (g3->rtype == GLF3_RTYPE_SUB) r += bgzf_write(fp, g3->lk, 10);
- else {
- int16_t x[2];
- r += bgzf_write(fp, g3->lk, 3);
- x[0] = glf3_is_BE? bam_swap_endian_2(g3->indel_len[0]) : g3->indel_len[0];
- x[1] = glf3_is_BE? bam_swap_endian_2(g3->indel_len[1]) : g3->indel_len[1];
- r += bgzf_write(fp, x, 4);
- if (g3->indel_len[0]) r += bgzf_write(fp, g3->indel_seq[0], abs(g3->indel_len[0]));
- if (g3->indel_len[1]) r += bgzf_write(fp, g3->indel_seq[1], abs(g3->indel_len[1]));
- }
- return r;
-}
-
-#ifndef kv_roundup32
-#define kv_roundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-int glf3_read1(glfFile fp, glf3_t *g3)
-{
- int r;
- uint8_t c;
- uint32_t y[2];
- r = bgzf_read(fp, &c, 1);
- if (r == 0) return 0;
- g3->ref_base = c & 0xf;
- g3->rtype = c>>4;
- if (g3->rtype == GLF3_RTYPE_END) return r;
- r += bgzf_read(fp, y, 8);
- if (glf3_is_BE) {
- y[0] = bam_swap_endian_4(y[0]);
- y[1] = bam_swap_endian_4(y[1]);
- }
- g3->offset = y[0];
- g3->min_lk = y[1]>>24;
- g3->depth = y[1]<<8>>8;
- r += bgzf_read(fp, &g3->rms_mapQ, 1);
- if (g3->rtype == GLF3_RTYPE_SUB) r += bgzf_read(fp, g3->lk, 10);
- else {
- int16_t x[2], max;
- r += bgzf_read(fp, g3->lk, 3);
- r += bgzf_read(fp, x, 4);
- if (glf3_is_BE) {
- x[0] = bam_swap_endian_2(x[0]);
- x[1] = bam_swap_endian_2(x[1]);
- }
- g3->indel_len[0] = x[0];
- g3->indel_len[1] = x[1];
- x[0] = abs(x[0]); x[1] = abs(x[1]);
- max = (x[0] > x[1]? x[0] : x[1]) + 1;
- if (g3->max_len < max) {
- g3->max_len = max;
- kv_roundup32(g3->max_len);
- g3->indel_seq[0] = (char*)realloc(g3->indel_seq[0], g3->max_len);
- g3->indel_seq[1] = (char*)realloc(g3->indel_seq[1], g3->max_len);
- }
- r += bgzf_read(fp, g3->indel_seq[0], x[0]);
- r += bgzf_read(fp, g3->indel_seq[1], x[1]);
- g3->indel_seq[0][x[0]] = g3->indel_seq[1][x[1]] = 0;
- }
- return r;
-}
-
-void glf3_view(glfFile fp)
-{
- glf3_header_t *h;
- char *name;
- glf3_t *g3;
- int len;
- h = glf3_header_read(fp);
- g3 = glf3_init1();
- while ((name = glf3_ref_read(fp, &len)) != 0) {
- int pos = 0;
- while (glf3_read1(fp, g3) && g3->rtype != GLF3_RTYPE_END) {
- pos += g3->offset;
- glf3_view1(name, g3, pos);
- }
- free(name);
- }
- glf3_header_destroy(h);
- glf3_destroy1(g3);
-}
-
-int glf3_view_main(int argc, char *argv[])
-{
- glfFile fp;
- if (argc == 1) {
- fprintf(pysamerr, "Usage: glfview <in.glf>\n");
- return 1;
- }
- fp = (strcmp(argv[1], "-") == 0)? bgzf_fdopen(fileno(stdin), "r") : bgzf_open(argv[1], "r");
- if (fp == 0) {
- fprintf(pysamerr, "Fail to open file '%s'\n", argv[1]);
- return 1;
- }
- glf3_view(fp);
- bgzf_close(fp);
- return 0;
-}
-
-#ifdef GLFVIEW_MAIN
-int main(int argc, char *argv[])
-{
- return glf3_view_main(argc, argv);
-}
-#endif
+++ /dev/null
-#ifndef GLF_H_
-#define GLF_H_
-
-typedef struct {
- unsigned char ref_base:4, dummy:4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
- unsigned char max_mapQ; /** maximum mapping quality */
- unsigned char lk[10]; /** log likelihood ratio, capped at 255 */
- unsigned min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
-} glf1_t;
-
-#include <stdint.h>
-#include "bgzf.h"
-typedef BGZF *glfFile;
-
-#define GLF3_RTYPE_END 0
-#define GLF3_RTYPE_SUB 1
-#define GLF3_RTYPE_INDEL 2
-
-typedef struct {
- uint8_t ref_base:4, rtype:4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
- uint8_t rms_mapQ; /** RMS mapping quality */
- uint8_t lk[10]; /** log likelihood ratio, capped at 255 */
- uint32_t min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
- int32_t offset; /** the first base in a chromosome has offset zero. */
- // for indel (lkHom1, lkHom2 and lkHet are the first three elements in lk[10])
- int16_t indel_len[2];
- int32_t max_len; // maximum indel len; will be modified by glf3_read1()
- char *indel_seq[2];
-} glf3_t;
-
-typedef struct {
- int32_t l_text;
- uint8_t *text;
-} glf3_header_t;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#define glf3_init1() ((glf3_t*)calloc(1, sizeof(glf3_t)))
-#define glf3_destroy1(g3) do { free((g3)->indel_seq[0]); free((g3)->indel_seq[1]); free(g3); } while (0)
-
- glf3_header_t *glf3_header_init();
- glf3_header_t *glf3_header_read(glfFile fp);
- void glf3_header_write(glfFile fp, const glf3_header_t *h);
- void glf3_header_destroy(glf3_header_t *h);
- char *glf3_ref_read(glfFile fp, int *len);
- void glf3_ref_write(glfFile fp, const char *name, int len);
- int glf3_write1(glfFile fp, const glf3_t *g3);
- int glf3_read1(glfFile fp, glf3_t *g3);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
double p = 1., Pr1 = 0.;
for (i = 0; i <= l_query + 1; ++i) {
p *= s[i];
- if (p < 1e-100) Pr += -4.343 * log(p), p = 1.;
+ if (p < 1e-100) Pr1 += -4.343 * log(p), p = 1.;
}
Pr1 += -4.343 * log(p * l_ref * l_query);
Pr = (int)(Pr1 + .499);
/* The MIT License
- Copyright (c) 2008 Genome Research Ltd (GRL).
+ Copyright (c) 2008, 2009, 2011 Attractive Chaos <attractor@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
SOFTWARE.
*/
-/* Contact: Heng Li <lh3@sanger.ac.uk> */
-
-/*
- 2009-07-16 (lh3): in kstream_t, change "char*" to "unsigned char*"
- */
-
-/* Last Modified: 12APR2009 */
+/* Last Modified: 18AUG2011 */
#ifndef AC_KSEQ_H
#define AC_KSEQ_H
#endif
#define __KS_GETUNTIL(__read, __bufsize) \
- static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
+ static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
{ \
if (dret) *dret = 0; \
- str->l = 0; \
+ str->l = append? str->l : 0; \
if (ks->begin >= ks->end && ks->is_eof) return -1; \
for (;;) { \
int i; \
break; \
} \
} \
- if (str->l == 0) { \
+ if (str->s == 0) { \
str->m = 1; \
str->s = (char*)calloc(1, 1); \
} \
str->s[str->l] = '\0'; \
return str->l; \
- }
+ } \
+ static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
+ { return ks_getuntil2(ks, delimiter, str, dret, 0); }
#define KSTREAM_INIT(type_t, __read, __bufsize) \
__KS_TYPE(type_t) \
-1 end-of-file
-2 truncated quality string
*/
-#define __KSEQ_READ \
- static int kseq_read(kseq_t *seq) \
- { \
- int c; \
- kstream_t *ks = seq->f; \
+#define __KSEQ_READ \
+ static int kseq_read(kseq_t *seq) \
+ { \
+ int c; \
+ kstream_t *ks = seq->f; \
if (seq->last_char == 0) { /* then jump to the next header line */ \
- while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
- if (c == -1) return -1; /* end of file */ \
- seq->last_char = c; \
- } /* the first header char has been read */ \
- seq->comment.l = seq->seq.l = seq->qual.l = 0; \
- if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; \
- if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); \
+ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
+ if (c == -1) return -1; /* end of file */ \
+ seq->last_char = c; \
+ } /* else: the first header char has been read in the previous call */ \
+ seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
+ if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
+ if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); /* read FASTA/Q comment */ \
+ if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
+ seq->seq.m = 256; \
+ seq->seq.s = (char*)malloc(seq->seq.m); \
+ } \
while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
- if (isgraph(c)) { /* printable non-space character */ \
- if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \
- seq->seq.m = seq->seq.l + 2; \
- kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \
- seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
- } \
- seq->seq.s[seq->seq.l++] = (char)c; \
- } \
- } \
+ seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
+ ks_getuntil2(ks, '\n', &seq->seq, 0, 1); /* read the rest of the line */ \
+ } \
if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
- seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
- if (c != '+') return seq->seq.l; /* FASTA */ \
- if (seq->qual.m < seq->seq.m) { /* allocate enough memory */ \
- seq->qual.m = seq->seq.m; \
- seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
- } \
+ if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
+ seq->seq.m = seq->seq.l + 2; \
+ kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \
+ seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
+ } \
+ seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
+ if (c != '+') return seq->seq.l; /* FASTA */ \
+ if (seq->qual.m < seq->seq.m) { /* allocate memory for qual in case insufficient */ \
+ seq->qual.m = seq->seq.m; \
+ seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
+ } \
while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
- if (c == -1) return -2; /* we should not stop here */ \
- while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l) \
- if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c; \
- seq->qual.s[seq->qual.l] = 0; /* null terminated string */ \
+ if (c == -1) return -2; /* error: no quality string */ \
+ while (ks_getuntil2(ks, '\n', &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
seq->last_char = 0; /* we have not come to the next header line */ \
- if (seq->seq.l != seq->qual.l) return -2; /* qual string is shorter than seq string */ \
- return seq->seq.l; \
+ if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
+ return seq->seq.l; \
}
#define __KSEQ_TYPE(type_t) \
} kseq_t;
#define KSEQ_INIT(type_t, __read) \
- KSTREAM_INIT(type_t, __read, 4096) \
+ KSTREAM_INIT(type_t, __read, 16384) \
__KSEQ_TYPE(type_t) \
__KSEQ_BASIC(type_t) \
__KSEQ_READ
--- /dev/null
+#include "pysam.h"
+
+#include <stdio.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <zlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <limits.h>
+
+#include "kseq.h"
+KSEQ_INIT(gzFile, gzread)
+
+typedef struct {
+ int n, m;
+ uint64_t *a;
+} reglist_t;
+
+#include "khash.h"
+KHASH_MAP_INIT_STR(reg, reglist_t)
+
+typedef kh_reg_t reghash_t;
+
+reghash_t *stk_reg_read(const char *fn)
+{
+ reghash_t *h = kh_init(reg);
+ gzFile fp;
+ kstream_t *ks;
+ int dret;
+ kstring_t *str;
+ // read the list
+ str = calloc(1, sizeof(kstring_t));
+ fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+ int beg = -1, end = -1;
+ reglist_t *p;
+ khint_t k = kh_get(reg, h, str->s);
+ if (k == kh_end(h)) {
+ int ret;
+ char *s = strdup(str->s);
+ k = kh_put(reg, h, s, &ret);
+ memset(&kh_val(h, k), 0, sizeof(reglist_t));
+ }
+ p = &kh_val(h, k);
+ if (dret != '\n') {
+ if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
+ beg = atoi(str->s);
+ if (dret != '\n') {
+ if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
+ end = atoi(str->s);
+ if (end < 0) end = -1;
+ }
+ }
+ }
+ }
+ // skip the rest of the line
+ if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
+ if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column
+ if (beg < 0) beg = 0, end = INT_MAX;
+ if (p->n == p->m) {
+ p->m = p->m? p->m<<1 : 4;
+ p->a = realloc(p->a, p->m * 8);
+ }
+ p->a[p->n++] = (uint64_t)beg<<32 | end;
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(str->s); free(str);
+ return h;
+}
+
+void stk_reg_destroy(reghash_t *h)
+{
+ khint_t k;
+ for (k = 0; k < kh_end(h); ++k) {
+ if (kh_exist(h, k)) {
+ free(kh_val(h, k).a);
+ free((char*)kh_key(h, k));
+ }
+ }
+ kh_destroy(reg, h);
+}
+
+/* constant table */
+
+unsigned char seq_nt16_table[256] = {
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15 /*'-'*/,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
+ 15,15, 5, 6, 8,15, 7, 9, 0,10,15,15, 15,15,15,15,
+ 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
+ 15,15, 5, 6, 8,15, 7, 9, 0,10,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
+};
+
+char *seq_nt16_rev_table = "XACMGRSVTWYHKDBN";
+unsigned char seq_nt16to4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
+int bitcnt_table[] = { 4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 };
+
+/* composition */
+int stk_comp(int argc, char *argv[])
+{
+ gzFile fp;
+ kseq_t *seq;
+ int l, c, upper_only = 0;
+ reghash_t *h = 0;
+ reglist_t dummy;
+ while ((c = getopt(argc, argv, "ur:")) >= 0) {
+ switch (c) {
+ case 'u': upper_only = 1; break;
+ case 'r': h = stk_reg_read(optarg); break;
+ }
+ }
+ if (argc == optind) {
+ fprintf(pysamerr, "Usage: seqtk comp [-u] [-r in.bed] <in.fa>\n\n");
+ fprintf(pysamerr, "Output format: chr, length, #A, #C, #G, #T, #2, #3, #4, #CpG, #tv, #ts, #CpG-ts\n");
+ return 1;
+ }
+ fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
+ seq = kseq_init(fp);
+ dummy.n= dummy.m = 1; dummy.a = calloc(1, 8);
+ while ((l = kseq_read(seq)) >= 0) {
+ int i, k;
+ reglist_t *p = 0;
+ if (h) {
+ khint_t k = kh_get(reg, h, seq->name.s);
+ if (k != kh_end(h)) p = &kh_val(h, k);
+ } else {
+ p = &dummy;
+ dummy.a[0] = l;
+ }
+ for (k = 0; p && k < p->n; ++k) {
+ int beg = p->a[k]>>32, end = p->a[k]&0xffffffff;
+ int la, lb, lc, na, nb, nc, cnt[11];
+ if (beg > 0) la = seq->seq.s[beg-1], lb = seq_nt16_table[la], lc = bitcnt_table[lb];
+ else la = 'a', lb = -1, lc = 0;
+ na = seq->seq.s[beg]; nb = seq_nt16_table[na]; nc = bitcnt_table[nb];
+ memset(cnt, 0, 11 * sizeof(int));
+ for (i = beg; i < end; ++i) {
+ int is_CpG = 0, a, b, c;
+ a = na; b = nb; c = nc;
+ na = seq->seq.s[i+1]; nb = seq_nt16_table[na]; nc = bitcnt_table[nb];
+ if (b == 2 || b == 10) { // C or Y
+ if (nb == 4 || nb == 5) is_CpG = 1;
+ } else if (b == 4 || b == 5) { // G or R
+ if (lb == 2 || lb == 10) is_CpG = 1;
+ }
+ if (upper_only == 0 || isupper(a)) {
+ if (c > 1) ++cnt[c+2];
+ if (c == 1) ++cnt[seq_nt16to4_table[b]];
+ if (b == 10 || b == 5) ++cnt[9];
+ else if (c == 2) {
+ ++cnt[8];
+ }
+ if (is_CpG) {
+ ++cnt[7];
+ if (b == 10 || b == 5) ++cnt[10];
+ }
+ }
+ la = a; lb = b; lc = c;
+ }
+ if (h) printf("%s\t%d\t%d", seq->name.s, beg, end);
+ else printf("%s\t%d", seq->name.s, l);
+ for (i = 0; i < 11; ++i) printf("\t%d", cnt[i]);
+ putchar('\n');
+ }
+ fflush(stdout);
+ }
+ free(dummy.a);
+ kseq_destroy(seq);
+ gzclose(fp);
+ return 0;
+}
+
+int stk_randbase(int argc, char *argv[])
+{
+ gzFile fp;
+ kseq_t *seq;
+ int l;
+ if (argc == 1) {
+ fprintf(pysamerr, "Usage: seqtk randbase <in.fa>\n");
+ return 1;
+ }
+ fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
+ seq = kseq_init(fp);
+ while ((l = kseq_read(seq)) >= 0) {
+ int i;
+ printf(">%s", seq->name.s);
+ for (i = 0; i < l; ++i) {
+ int c, b, a, j, k, m;
+ b = seq->seq.s[i];
+ c = seq_nt16_table[b];
+ a = bitcnt_table[c];
+ if (a == 2) {
+ m = (drand48() < 0.5);
+ for (j = k = 0; j < 4; ++j) {
+ if ((1<<j & c) == 0) continue;
+ if (k == m) break;
+ ++k;
+ }
+ seq->seq.s[i] = islower(b)? "acgt"[j] : "ACGT"[j];
+ }
+ if (i%60 == 0) putchar('\n');
+ putchar(seq->seq.s[i]);
+ }
+ putchar('\n');
+ }
+ kseq_destroy(seq);
+ gzclose(fp);
+ return 0;
+}
+
+int stk_hety(int argc, char *argv[])
+{
+ gzFile fp;
+ kseq_t *seq;
+ int l, c, win_size = 50000, n_start = 5, win_step, is_lower_mask = 0;
+ char *buf;
+ uint32_t cnt[3];
+ if (argc == 1) {
+ fprintf(pysamerr, "\n");
+ fprintf(pysamerr, "Usage: seqtk hety [options] <in.fa>\n\n");
+ fprintf(pysamerr, "Options: -w INT window size [%d]\n", win_size);
+ fprintf(pysamerr, " -t INT # start positions in a window [%d]\n", n_start);
+ fprintf(pysamerr, " -m treat lowercases as masked\n");
+ fprintf(pysamerr, "\n");
+ return 1;
+ }
+ while ((c = getopt(argc, argv, "w:t:m")) >= 0) {
+ switch (c) {
+ case 'w': win_size = atoi(optarg); break;
+ case 't': n_start = atoi(optarg); break;
+ case 'm': is_lower_mask = 1; break;
+ }
+ }
+ fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
+ seq = kseq_init(fp);
+ win_step = win_size / n_start;
+ buf = calloc(win_size, 1);
+ while ((l = kseq_read(seq)) >= 0) {
+ int x, i, y, z, next = 0;
+ cnt[0] = cnt[1] = cnt[2] = 0;
+ for (i = 0; i <= l; ++i) {
+ if ((i >= win_size && i % win_step == 0) || i == l) {
+ if (i == l && l >= win_size) {
+ for (y = l - win_size; y < next; ++y) --cnt[(int)buf[y % win_size]];
+ }
+ if (cnt[1] + cnt[2] > 0)
+ printf("%s\t%d\t%d\t%.2lf\t%d\t%d\n", seq->name.s, next, i,
+ (double)cnt[2] / (cnt[1] + cnt[2]) * win_size, cnt[1] + cnt[2], cnt[2]);
+ next = i;
+ }
+ if (i < l) {
+ y = i % win_size;
+ c = seq->seq.s[i];
+ if (is_lower_mask && islower(c)) c = 'N';
+ c = seq_nt16_table[c];
+ x = bitcnt_table[c];
+ if (i >= win_size) --cnt[(int)buf[y]];
+ buf[y] = z = x > 2? 0 : x == 2? 2 : 1;
+ ++cnt[z];
+ }
+ }
+ }
+ free(buf);
+ kseq_destroy(seq);
+ gzclose(fp);
+ return 0;
+}
+
+/* fq2fa */
+int stk_fq2fa(int argc, char *argv[])
+{
+ gzFile fp;
+ kseq_t *seq;
+ char *buf;
+ int l, i, c, qual_thres = 0, linelen = 60;
+ while ((c = getopt(argc, argv, "q:l:")) >= 0) {
+ switch (c) {
+ case 'q': qual_thres = atoi(optarg); break;
+ case 'l': linelen = atoi(optarg); break;
+ }
+ }
+ if (argc == optind) {
+ fprintf(pysamerr, "Usage: seqtk fq2fa [-q qualThres=0] [-l lineLen=60] <in.fq>\n");
+ return 1;
+ }
+ buf = linelen > 0? malloc(linelen + 1) : 0;
+ fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
+ seq = kseq_init(fp);
+ while ((l = kseq_read(seq)) >= 0) {
+ if (seq->qual.l && qual_thres > 0) {
+ for (i = 0; i < l; ++i)
+ if (seq->qual.s[i] - 33 < qual_thres)
+ seq->seq.s[i] = tolower(seq->seq.s[i]);
+ }
+ putchar('>');
+ if (seq->comment.l) {
+ fputs(seq->name.s, stdout);
+ putchar(' ');
+ puts(seq->comment.s);
+ } else puts(seq->name.s);
+ if (buf) { // multi-line
+ for (i = 0; i < l; i += linelen) {
+ int x = i + linelen < l? linelen : l - i;
+ memcpy(buf, seq->seq.s + i, x);
+ buf[x] = 0;
+ puts(buf);
+ }
+ } else puts(seq->seq.s);
+ }
+ free(buf);
+ kseq_destroy(seq);
+ gzclose(fp);
+ return 0;
+}
+
+int stk_maskseq(int argc, char *argv[])
+{
+ khash_t(reg) *h = kh_init(reg);
+ gzFile fp;
+ kseq_t *seq;
+ int l, i, j, c, is_complement = 0, is_lower = 0;
+ khint_t k;
+ while ((c = getopt(argc, argv, "cl")) >= 0) {
+ switch (c) {
+ case 'c': is_complement = 1; break;
+ case 'l': is_lower = 1; break;
+ }
+ }
+ if (argc - optind < 2) {
+ fprintf(pysamerr, "Usage: seqtk maskseq [-cl] <in.fa> <in.bed>\n\n");
+ fprintf(pysamerr, "Options: -c mask the complement regions\n");
+ fprintf(pysamerr, " -l soft mask (to lower cases)\n");
+ return 1;
+ }
+ h = stk_reg_read(argv[optind+1]);
+ // maskseq
+ fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
+ seq = kseq_init(fp);
+ while ((l = kseq_read(seq)) >= 0) {
+ k = kh_get(reg, h, seq->name.s);
+ if (k == kh_end(h)) { // not found in the hash table
+ if (is_complement) {
+ for (j = 0; j < l; ++j)
+ seq->seq.s[j] = is_lower? tolower(seq->seq.s[j]) : 'N';
+ }
+ } else {
+ reglist_t *p = &kh_val(h, k);
+ if (!is_complement) {
+ for (i = 0; i < p->n; ++i) {
+ int beg = p->a[i]>>32, end = p->a[i];
+ if (beg >= seq->seq.l) {
+ fprintf(pysamerr, "[maskseq] start position >= the sequence length.\n");
+ continue;
+ }
+ if (end >= seq->seq.l) end = seq->seq.l;
+ if (is_lower) for (j = beg; j < end; ++j) seq->seq.s[j] = tolower(seq->seq.s[j]);
+ else for (j = beg; j < end; ++j) seq->seq.s[j] = 'N';
+ }
+ } else {
+ int8_t *mask = calloc(seq->seq.l, 1);
+ for (i = 0; i < p->n; ++i) {
+ int beg = p->a[i]>>32, end = p->a[i];
+ if (end >= seq->seq.l) end = seq->seq.l;
+ for (j = beg; j < end; ++j) mask[j] = 1;
+ }
+ for (j = 0; j < l; ++j)
+ if (mask[j] == 0) seq->seq.s[j] = is_lower? tolower(seq->seq.s[j]) : 'N';
+ free(mask);
+ }
+ }
+ printf(">%s", seq->name.s);
+ for (j = 0; j < seq->seq.l; ++j) {
+ if (j%60 == 0) putchar('\n');
+ putchar(seq->seq.s[j]);
+ }
+ putchar('\n');
+ }
+ // free
+ kseq_destroy(seq);
+ gzclose(fp);
+ stk_reg_destroy(h);
+ return 0;
+}
+
+/* subseq */
+
+int stk_subseq(int argc, char *argv[])
+{
+ khash_t(reg) *h = kh_init(reg);
+ gzFile fp;
+ kseq_t *seq;
+ int l, i, j, c, is_tab = 0;
+ khint_t k;
+ while ((c = getopt(argc, argv, "t")) >= 0) {
+ switch (c) {
+ case 't': is_tab = 1; break;
+ }
+ }
+ if (optind + 2 > argc) {
+ fprintf(pysamerr, "Usage: seqtk subseq [-t] <in.fa> <in.bed>\n\n");
+ fprintf(pysamerr, "Note: Use 'samtools faidx' if only a few regions are intended.\n");
+ return 1;
+ }
+ h = stk_reg_read(argv[optind+1]);
+ // subseq
+ fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
+ seq = kseq_init(fp);
+ while ((l = kseq_read(seq)) >= 0) {
+ reglist_t *p;
+ k = kh_get(reg, h, seq->name.s);
+ if (k == kh_end(h)) continue;
+ p = &kh_val(h, k);
+ for (i = 0; i < p->n; ++i) {
+ int beg = p->a[i]>>32, end = p->a[i];
+ if (beg >= seq->seq.l) {
+ fprintf(pysamerr, "[subseq] %s: %d >= %ld\n", seq->name.s, beg, seq->seq.l);
+ continue;
+ }
+ if (end > seq->seq.l) end = seq->seq.l;
+ if (is_tab == 0) {
+ printf("%c%s", seq->qual.l == seq->seq.l? '@' : '>', seq->name.s);
+ if (end == INT_MAX) {
+ if (beg) printf(":%d", beg+1);
+ } else printf(":%d-%d", beg+1, end);
+ } else printf("%s\t%d\t", seq->name.s, beg + 1);
+ if (end > seq->seq.l) end = seq->seq.l;
+ for (j = 0; j < end - beg; ++j) {
+ if (is_tab == 0 && j % 60 == 0) putchar('\n');
+ putchar(seq->seq.s[j + beg]);
+ }
+ putchar('\n');
+ if (seq->qual.l != seq->seq.l || is_tab) continue;
+ printf("+");
+ for (j = 0; j < end - beg; ++j) {
+ if (j % 60 == 0) putchar('\n');
+ putchar(seq->qual.s[j + beg]);
+ }
+ putchar('\n');
+ }
+ }
+ // free
+ kseq_destroy(seq);
+ gzclose(fp);
+ stk_reg_destroy(h);
+ return 0;
+}
+
+/* mergefa */
+int stk_mergefa(int argc, char *argv[])
+{
+ gzFile fp[2];
+ kseq_t *seq[2];
+ int i, l, c, is_intersect = 0, is_haploid = 0, qual = 0, is_mask = 0;
+ while ((c = getopt(argc, argv, "himq:")) >= 0) {
+ switch (c) {
+ case 'i': is_intersect = 1; break;
+ case 'h': is_haploid = 1; break;
+ case 'm': is_mask = 1; break;
+ case 'q': qual = atoi(optarg); break;
+ }
+ }
+ if (is_mask && is_intersect) {
+ fprintf(pysamerr, "[%s] `-i' and `-h' cannot be applied at the same time.\n", __func__);
+ return 1;
+ }
+ if (optind + 2 > argc) {
+ fprintf(pysamerr, "\nUsage: seqtk mergefa [options] <in1.fa> <in2.fa>\n\n");
+ fprintf(pysamerr, "Options: -q INT quality threshold [0]\n");
+ fprintf(pysamerr, " -i take intersection\n");
+ fprintf(pysamerr, " -m convert to lowercase when one of the input base is N.\n");
+ fprintf(pysamerr, " -h suppress hets in the input\n\n");
+ return 1;
+ }
+ for (i = 0; i < 2; ++i) {
+ fp[i] = strcmp(argv[optind+i], "-")? gzopen(argv[optind+i], "r") : gzdopen(fileno(stdin), "r");
+ seq[i] = kseq_init(fp[i]);
+ }
+ while (kseq_read(seq[0]) >= 0) {
+ int min_l, c[2], is_upper;
+ kseq_read(seq[1]);
+ if (strcmp(seq[0]->name.s, seq[1]->name.s))
+ fprintf(pysamerr, "[%s] Different sequence names: %s != %s\n", __func__, seq[0]->name.s, seq[1]->name.s);
+ if (seq[0]->seq.l != seq[1]->seq.l)
+ fprintf(pysamerr, "[%s] Unequal sequence length: %ld != %ld\n", __func__, seq[0]->seq.l, seq[1]->seq.l);
+ min_l = seq[0]->seq.l < seq[1]->seq.l? seq[0]->seq.l : seq[1]->seq.l;
+ printf(">%s", seq[0]->name.s);
+ for (l = 0; l < min_l; ++l) {
+ c[0] = seq[0]->seq.s[l]; c[1] = seq[1]->seq.s[l];
+ if (seq[0]->qual.l && seq[0]->qual.s[l] - 33 < qual) c[0] = tolower(c[0]);
+ if (seq[1]->qual.l && seq[1]->qual.s[l] - 33 < qual) c[1] = tolower(c[1]);
+ if (is_intersect) is_upper = (isupper(c[0]) || isupper(c[1]))? 1 : 0;
+ else if (is_mask) is_upper = (isupper(c[0]) || isupper(c[1]))? 1 : 0;
+ else is_upper = (isupper(c[0]) && isupper(c[1]))? 1 : 0;
+ c[0] = seq_nt16_table[c[0]]; c[1] = seq_nt16_table[c[1]];
+ if (c[0] == 0) c[0] = 15;
+ if (c[1] == 0) c[1] = 15;
+ if (is_haploid && (bitcnt_table[c[0]] > 1 || bitcnt_table[c[1]] > 1)) is_upper = 0;
+ if (is_intersect) {
+ c[0] = c[0] & c[1];
+ if (c[0] == 0) is_upper = 0;
+ } else if (is_mask) {
+ if (c[0] == 15 || c[1] == 15) is_upper = 0;
+ c[0] = c[0] & c[1];
+ if (c[0] == 0) is_upper = 0;
+ } else c[0] = c[0] | c[1];
+ c[0] = seq_nt16_rev_table[c[0]];
+ if (!is_upper) c[0] = tolower(c[0]);
+ if (l%60 == 0) putchar('\n');
+ putchar(c[0]);
+ }
+ putchar('\n');
+ }
+ return 0;
+}
+
+int stk_famask(int argc, char *argv[])
+{
+ gzFile fp[2];
+ kseq_t *seq[2];
+ int i, l;
+ if (argc < 3) {
+ fprintf(pysamerr, "Usage: seqtk famask <src.fa> <mask.fa>\n");
+ return 1;
+ }
+ for (i = 0; i < 2; ++i) {
+ fp[i] = strcmp(argv[optind+i], "-")? gzopen(argv[optind+i], "r") : gzdopen(fileno(stdin), "r");
+ seq[i] = kseq_init(fp[i]);
+ }
+ while (kseq_read(seq[0]) >= 0) {
+ int min_l, c[2];
+ kseq_read(seq[1]);
+ if (strcmp(seq[0]->name.s, seq[1]->name.s))
+ fprintf(pysamerr, "[%s] Different sequence names: %s != %s\n", __func__, seq[0]->name.s, seq[1]->name.s);
+ if (seq[0]->seq.l != seq[1]->seq.l)
+ fprintf(pysamerr, "[%s] Unequal sequence length: %ld != %ld\n", __func__, seq[0]->seq.l, seq[1]->seq.l);
+ min_l = seq[0]->seq.l < seq[1]->seq.l? seq[0]->seq.l : seq[1]->seq.l;
+ printf(">%s", seq[0]->name.s);
+ for (l = 0; l < min_l; ++l) {
+ c[0] = seq[0]->seq.s[l]; c[1] = seq[1]->seq.s[l];
+ if (c[1] == 'x') c[0] = tolower(c[0]);
+ else if (c[1] != 'X') c[0] = c[1];
+ if (l%60 == 0) putchar('\n');
+ putchar(c[0]);
+ }
+ putchar('\n');
+ }
+ return 0;
+}
+
+int stk_mutfa(int argc, char *argv[])
+{
+ khash_t(reg) *h = kh_init(reg);
+ gzFile fp;
+ kseq_t *seq;
+ kstream_t *ks;
+ int l, i, dret;
+ kstring_t *str;
+ khint_t k;
+ if (argc < 3) {
+ fprintf(pysamerr, "Usage: seqtk mutfa <in.fa> <in.snp>\n\n");
+ fprintf(pysamerr, "Note: <in.snp> contains at least four columns per line which are:\n");
+ fprintf(pysamerr, " 'chr 1-based-pos any base-changed-to'.\n");
+ return 1;
+ }
+ // read the list
+ str = calloc(1, sizeof(kstring_t));
+ fp = strcmp(argv[2], "-")? gzopen(argv[2], "r") : gzdopen(fileno(stdin), "r");
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+ char *s = strdup(str->s);
+ int beg = 0, ret;
+ reglist_t *p;
+ k = kh_get(reg, h, s);
+ if (k == kh_end(h)) {
+ k = kh_put(reg, h, s, &ret);
+ memset(&kh_val(h, k), 0, sizeof(reglist_t));
+ }
+ p = &kh_val(h, k);
+ if (ks_getuntil(ks, 0, str, &dret) > 0) beg = atol(str->s) - 1; // 2nd col
+ ks_getuntil(ks, 0, str, &dret); // 3rd col
+ ks_getuntil(ks, 0, str, &dret); // 4th col
+ // skip the rest of the line
+ if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
+ if (isalpha(str->s[0]) && str->l == 1) {
+ if (p->n == p->m) {
+ p->m = p->m? p->m<<1 : 4;
+ p->a = realloc(p->a, p->m * 8);
+ }
+ p->a[p->n++] = (uint64_t)beg<<32 | str->s[0];
+ }
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(str->s); free(str);
+ // mutfa
+ fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
+ seq = kseq_init(fp);
+ while ((l = kseq_read(seq)) >= 0) {
+ reglist_t *p;
+ k = kh_get(reg, h, seq->name.s);
+ if (k != kh_end(h)) {
+ p = &kh_val(h, k);
+ for (i = 0; i < p->n; ++i) {
+ int beg = p->a[i]>>32;
+ if (beg < seq->seq.l)
+ seq->seq.s[beg] = (int)p->a[i];
+ }
+ }
+ printf(">%s", seq->name.s);
+ for (i = 0; i < l; ++i) {
+ if (i%60 == 0) putchar('\n');
+ putchar(seq->seq.s[i]);
+ }
+ putchar('\n');
+ }
+ // free
+ kseq_destroy(seq);
+ gzclose(fp);
+ for (k = 0; k < kh_end(h); ++k) {
+ if (kh_exist(h, k)) {
+ free(kh_val(h, k).a);
+ free((char*)kh_key(h, k));
+ }
+ }
+ kh_destroy(reg, h);
+ return 0;
+}
+
+int stk_listhet(int argc, char *argv[])
+{
+ gzFile fp;
+ kseq_t *seq;
+ int i, l;
+ if (argc == 1) {
+ fprintf(pysamerr, "Usage: seqtk listhet <in.fa>\n");
+ return 1;
+ }
+ fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
+ seq = kseq_init(fp);
+ while ((l = kseq_read(seq)) >= 0) {
+ for (i = 0; i < l; ++i) {
+ int b = seq->seq.s[i];
+ if (bitcnt_table[seq_nt16_table[b]] == 2)
+ printf("%s\t%d\t%c\n", seq->name.s, i+1, b);
+ }
+ }
+ kseq_destroy(seq);
+ gzclose(fp);
+ return 0;
+}
+
+/* cutN */
+static int cutN_min_N_tract = 1000;
+static int cutN_nonN_penalty = 10;
+
+static int find_next_cut(const kseq_t *ks, int k, int *begin, int *end)
+{
+ int i, b, e;
+ while (k < ks->seq.l) {
+ if (seq_nt16_table[(int)ks->seq.s[k]] == 15) {
+ int score, max;
+ score = 0; e = max = -1;
+ for (i = k; i < ks->seq.l && score >= 0; ++i) { /* forward */
+ if (seq_nt16_table[(int)ks->seq.s[i]] == 15) ++score;
+ else score -= cutN_nonN_penalty;
+ if (score > max) max = score, e = i;
+ }
+ score = 0; b = max = -1;
+ for (i = e; i >= 0 && score >= 0; --i) { /* backward */
+ if (seq_nt16_table[(int)ks->seq.s[i]] == 15) ++score;
+ else score -= cutN_nonN_penalty;
+ if (score > max) max = score, b = i;
+ }
+ if (e + 1 - b >= cutN_min_N_tract) {
+ *begin = b;
+ *end = e + 1;
+ return *end;
+ }
+ k = e + 1;
+ } else ++k;
+ }
+ return -1;
+}
+static void print_seq(FILE *fpout, const kseq_t *ks, int begin, int end)
+{
+ int i;
+ if (begin >= end) return; // FIXME: why may this happen? Understand it!
+ fprintf(fpout, ">%s:%d-%d", ks->name.s, begin+1, end);
+ for (i = begin; i < end && i < ks->seq.l; ++i) {
+ if ((i - begin)%60 == 0) fputc('\n', fpout);
+ fputc(ks->seq.s[i], fpout);
+ }
+ fputc('\n', fpout);
+}
+int stk_cutN(int argc, char *argv[])
+{
+ int c, l, gap_only = 0;
+ gzFile fp;
+ kseq_t *ks;
+ while ((c = getopt(argc, argv, "n:p:g")) >= 0) {
+ switch (c) {
+ case 'n': cutN_min_N_tract = atoi(optarg); break;
+ case 'p': cutN_nonN_penalty = atoi(optarg); break;
+ case 'g': gap_only = 1; break;
+ default: return 1;
+ }
+ }
+ if (argc == optind) {
+ fprintf(pysamerr, "\n");
+ fprintf(pysamerr, "Usage: seqtk cutN [options] <in.fa>\n\n");
+ fprintf(pysamerr, "Options: -n INT min size of N tract [%d]\n", cutN_min_N_tract);
+ fprintf(pysamerr, " -p INT penalty for a non-N [%d]\n", cutN_nonN_penalty);
+ fprintf(pysamerr, " -g print gaps only, no sequence\n\n");
+ return 1;
+ }
+ fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
+ ks = kseq_init(fp);
+ while ((l = kseq_read(ks)) >= 0) {
+ int k = 0, begin = 0, end = 0;
+ while (find_next_cut(ks, k, &begin, &end) >= 0) {
+ if (begin != 0) {
+ if (gap_only) printf("%s\t%d\t%d\n", ks->name.s, begin, end);
+ else print_seq(stdout, ks, k, begin);
+ }
+ k = end;
+ }
+ if (!gap_only) print_seq(stdout, ks, k, l);
+ }
+ kseq_destroy(ks);
+ gzclose(fp);
+ return 0;
+}
+
+/* main function */
+static int usage()
+{
+ fprintf(pysamerr, "\n");
+ fprintf(pysamerr, "Usage: seqtk <command> <arguments>\n\n");
+ fprintf(pysamerr, "Command: comp get the nucleotide composite of FASTA/Q\n");
+ fprintf(pysamerr, " hety regional heterozygosity\n");
+ fprintf(pysamerr, " fq2fa convert FASTQ to FASTA\n");
+ fprintf(pysamerr, " subseq extract subsequences from FASTA/Q\n");
+ fprintf(pysamerr, " maskseq mask sequences\n");
+ fprintf(pysamerr, " mutfa point mutate FASTA at specified positions\n");
+ fprintf(pysamerr, " mergefa merge two FASTA/Q files\n");
+ fprintf(pysamerr, " randbase choose a random base from hets\n");
+ fprintf(pysamerr, " cutN cut sequence at long N\n");
+ fprintf(pysamerr, " listhet extract the position of each het\n");
+ fprintf(pysamerr, "\n");
+ return 1;
+}
+
+int main(int argc, char *argv[])
+{
+ if (argc == 1) return usage();
+ if (strcmp(argv[1], "comp") == 0) stk_comp(argc-1, argv+1);
+ else if (strcmp(argv[1], "hety") == 0) stk_hety(argc-1, argv+1);
+ else if (strcmp(argv[1], "fq2fa") == 0) stk_fq2fa(argc-1, argv+1);
+ else if (strcmp(argv[1], "subseq") == 0) stk_subseq(argc-1, argv+1);
+ else if (strcmp(argv[1], "maskseq") == 0) stk_maskseq(argc-1, argv+1);
+ else if (strcmp(argv[1], "mutfa") == 0) stk_mutfa(argc-1, argv+1);
+ else if (strcmp(argv[1], "mergefa") == 0) stk_mergefa(argc-1, argv+1);
+ else if (strcmp(argv[1], "randbase") == 0) stk_randbase(argc-1, argv+1);
+ else if (strcmp(argv[1], "cutN") == 0) stk_cutN(argc-1, argv+1);
+ else if (strcmp(argv[1], "listhet") == 0) stk_listhet(argc-1, argv+1);
+ else if (strcmp(argv[1], "famask") == 0) stk_famask(argc-1, argv+1);
+ else {
+ fprintf(pysamerr, "[main] unrecognized commad '%s'. Abort!\n", argv[1]);
+ return 1;
+ }
+ return 0;
+}
+++ /dev/null
-// Windows-specific code, include with:\r
-// #ifdef _MSC_VER\r
-// #include <msvc_compat.h>\r
-// #endif\r
-\r
-//#define _CRT_SECURE_NO_WARNINGS\r
-#ifndef MSVC_COMPAT_H\r
-#define MSVC_COMPAT_H\r
-\r
-#define inline __inline\r
-#define __func__ __FUNCTION__\r
-\r
-#include <float.h>\r
-#define isnan _isnan\r
-static int isinf(double x) {\r
- int y = _finite(x);\r
- if(y == 0) {\r
- return 0;\r
- } else {\r
- return 1;\r
- }\r
-}\r
-#define alloca _alloca\r
-#define atoll _atoi64\r
-\r
-#define ftello ftell\r
-
-typedef int bool;\r
-\r
-static int R_OK = 4;
-\r
-#ifndef lgamma\r
-/* Log gamma function\r
- * \log{\Gamma(z)}\r
- * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245\r
- */\r
-static double lgamma(double z)\r
-{\r
- double x = 0;\r
- x += 0.1659470187408462e-06 / (z+7);\r
- x += 0.9934937113930748e-05 / (z+6);\r
- x -= 0.1385710331296526 / (z+5);\r
- x += 12.50734324009056 / (z+4);\r
- x -= 176.6150291498386 / (z+3);\r
- x += 771.3234287757674 / (z+2);\r
- x -= 1259.139216722289 / (z+1);\r
- x += 676.5203681218835 / z;\r
- x += 0.9999999999995183;\r
- return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5);\r
-}\r
-#endif\r
-\r
-#ifndef M_LN10\r
-#define M_LN10 2.30258509299404568402\r
-#endif\r
-#ifndef M_LN2\r
-#define M_LN2 0.69314718055994530942\r
-#endif\r
-
-#endif\r
typedef khash_t(rg) *rghash_t;
+// FIXME: we'd better use no global variables...
static rghash_t g_rghash = 0;
static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
+static float g_subsam = -1;
static char *g_library, *g_rg;
-static int g_sol2sanger_tbl[128];
static void *g_bed;
void *bed_read(const char *fn);
void bed_destroy(void *_h);
int bed_overlap(const void *_h, const char *chr, int beg, int end);
-static void sol2sanger(bam1_t *b)
-{
- int l;
- uint8_t *qual = bam1_qual(b);
- if (g_sol2sanger_tbl[30] == 0) {
- for (l = 0; l != 128; ++l) {
- g_sol2sanger_tbl[l] = (int)(10.0 * log(1.0 + pow(10.0, (l - 64 + 33) / 10.0)) / log(10.0) + .499);
- if (g_sol2sanger_tbl[l] >= 93) g_sol2sanger_tbl[l] = 93;
- }
- }
- for (l = 0; l < b->core.l_qseq; ++l) {
- int q = qual[l];
- if (q > 127) q = 127;
- qual[l] = g_sol2sanger_tbl[q];
- }
-}
-
static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
{
if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
return 1;
if (g_bed && b->core.tid >= 0 && !bed_overlap(g_bed, h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b))))
return 1;
+ if (g_subsam > 0.) {
+ int x = (int)(g_subsam + .499);
+ uint32_t k = __ac_X31_hash_string(bam1_qname(b)) + x;
+ if (k%1024 / 1024.0 >= g_subsam - x) return 1;
+ }
if (g_rg || g_rghash) {
uint8_t *s = bam_aux_get(b, "RG");
if (s) {
int main_samview(int argc, char *argv[])
{
- int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, slx2sngr = 0, is_count = 0;
+ int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0;
int of_type = BAM_OFDEC, is_long_help = 0;
int count = 0;
samfile_t *in = 0, *out = 0;
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
- while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:CR:L:")) >= 0) {
+ while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:")) >= 0) {
switch (c) {
+ case 's': g_subsam = atof(optarg); break;
case 'c': is_count = 1; break;
- case 'C': slx2sngr = 1; break;
case 'S': is_bamin = 0; break;
case 'b': is_bamout = 1; break;
case 't': fn_list = strdup(optarg); is_bamin = 0; break;
int r;
while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
if (!__g_skip_aln(in->header, b)) {
- if (slx2sngr) sol2sanger(b);
if (!is_count) samwrite(out, b); // write the alignment to `out'
count++;
}
fprintf(pysamerr, " -q INT minimum mapping quality [0]\n");
fprintf(pysamerr, " -l STR only output reads in library STR [null]\n");
fprintf(pysamerr, " -r STR only output reads in read group STR [null]\n");
+ fprintf(pysamerr, " -s FLOAT fraction of templates to subsample; integer part as seed [-1]\n");
fprintf(pysamerr, " -? longer help\n");
fprintf(pysamerr, "\n");
if (is_long_help)
free(argv2);
return ret;
}
+
+int8_t seq_comp_table[16] = { 0, 8, 4, 12, 2, 10, 9, 14, 1, 6, 5, 13, 3, 11, 7, 15 };
+
+int main_bam2fq(int argc, char *argv[])
+{
+ bamFile fp;
+ bam_header_t *h;
+ bam1_t *b;
+ int8_t *buf;
+ int max_buf;
+ if (argc == 1) {
+ fprintf(pysamerr, "Usage: samtools bam2fq <in.bam>\n");
+ return 1;
+ }
+ fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
+ if (fp == 0) return 1;
+ h = bam_header_read(fp);
+ b = bam_init1();
+ buf = 0;
+ max_buf = 0;
+ while (bam_read1(fp, b) >= 0) {
+ int i, qlen = b->core.l_qseq;
+ uint8_t *seq;
+ putchar('@'); fputs(bam1_qname(b), stdout);
+ if ((b->core.flag & 0x40) && !(b->core.flag & 0x80)) puts("/1");
+ else if ((b->core.flag & 0x80) && !(b->core.flag & 0x40)) puts("/2");
+ else putchar('\n');
+ if (max_buf < qlen + 1) {
+ max_buf = qlen + 1;
+ kroundup32(max_buf);
+ buf = realloc(buf, max_buf);
+ }
+ buf[qlen] = 0;
+ seq = bam1_seq(b);
+ for (i = 0; i < qlen; ++i)
+ buf[i] = bam1_seqi(seq, i);
+ if (b->core.flag & 16) { // reverse complement
+ for (i = 0; i < qlen>>1; ++i) {
+ int8_t t = seq_comp_table[buf[qlen - 1 - i]];
+ buf[qlen - 1 - i] = seq_comp_table[buf[i]];
+ buf[i] = t;
+ }
+ if (qlen&1) buf[i] = seq_comp_table[buf[i]];
+ }
+ for (i = 0; i < qlen; ++i)
+ buf[i] = bam_nt16_rev_table[buf[i]];
+ puts((char*)buf);
+ puts("+");
+ seq = bam1_qual(b);
+ for (i = 0; i < qlen; ++i)
+ buf[i] = 33 + seq[i];
+ if (b->core.flag & 16) { // reverse
+ for (i = 0; i < qlen>>1; ++i) {
+ int8_t t = buf[qlen - 1 - i];
+ buf[qlen - 1 - i] = buf[i];
+ buf[i] = t;
+ }
+ }
+ puts((char*)buf);
+ }
+ free(buf);
+ bam_destroy1(b);
+ bam_header_destroy(h);
+ bam_close(fp);
+ return 0;
+}
int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
{
const char *p = txt, *q, *r;
- kstring_t buf;
+ kstring_t buf, first_sm;
int n = 0;
khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id;
+ if (txt == 0) {
+ add_pair(sm, sm2id, fn, fn);
+ return 0;
+ }
memset(&buf, 0, sizeof(kstring_t));
+ memset(&first_sm, 0, sizeof(kstring_t));
while ((q = strstr(p, "@RG")) != 0) {
p = q + 3;
r = q = 0;
oq = *u; or = *v; *u = *v = '\0';
buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
add_pair(sm, sm2id, buf.s, r);
+ if ( !first_sm.s )
+ kputs(r,&first_sm);
*u = oq; *v = or;
} else break;
p = q > r? q : r;
++n;
}
if (n == 0) add_pair(sm, sm2id, fn, fn);
+ // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but
+ // use the tag instead.
+ else if ( n==1 && first_sm.s )
+ add_pair(sm,sm2id,fn,first_sm.s);
+ if ( first_sm.s )
+ free(first_sm.s);
+
// add_pair(sm, sm2id, fn, fn);
free(buf.s);
return 0;
version = version.__version__
samtools_exclude = ( "bamtk.c", "razip.c", "bgzip.c",
- "bam_reheader.c",
"main.c", "calDepth.c", "bam2bed.c",
"wgsim.c", "md5fa.c", "maq2sam.c",)
samtools_dest = os.path.abspath( "samtools" )
+++ /dev/null
-// Windows-specific code, include with:\r
-// #ifdef _MSC_VER\r
-// #include <msvc_compat.h>\r
-// #endif\r
-\r
-//#define _CRT_SECURE_NO_WARNINGS\r
-#ifndef MSVC_COMPAT_H\r
-#define MSVC_COMPAT_H\r
-\r
-#define inline __inline\r
-#define __func__ __FUNCTION__\r
-\r
-#include <float.h>\r
-#define isnan _isnan\r
-static int isinf(double x) {\r
- int y = _finite(x);\r
- if(y == 0) {\r
- return 0;\r
- } else {\r
- return 1;\r
- }\r
-}\r
-#define alloca _alloca\r
-#define atoll _atoi64\r
-\r
-#define ftello ftell\r
-
-typedef int bool;\r
-\r
-static int R_OK = 4;
-\r
-#ifndef lgamma\r
-/* Log gamma function\r
- * \log{\Gamma(z)}\r
- * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245\r
- */\r
-static double lgamma(double z)\r
-{\r
- double x = 0;\r
- x += 0.1659470187408462e-06 / (z+7);\r
- x += 0.9934937113930748e-05 / (z+6);\r
- x -= 0.1385710331296526 / (z+5);\r
- x += 12.50734324009056 / (z+4);\r
- x -= 176.6150291498386 / (z+3);\r
- x += 771.3234287757674 / (z+2);\r
- x -= 1259.139216722289 / (z+1);\r
- x += 676.5203681218835 / z;\r
- x += 0.9999999999995183;\r
- return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5);\r
-}\r
-#endif\r
-\r
-#ifndef M_LN10\r
-#define M_LN10 2.30258509299404568402\r
-#endif\r
-#ifndef M_LN2\r
-#define M_LN2 0.69314718055994530942\r
-#endif\r
-
-#endif\r
-import sys
+## This script contains some example code
+## illustrating ways to to use the pysam
+## interface to samtools.
+##
+## The unit tests in the script pysam_test.py
+## contain more examples.
+##
+
import pysam
samfile = pysam.Samfile( "ex1.bam", "rb" )
def my_pileup_callback( column ): print str(column)
samfile.pileup( region="chr1:10-200", callback=my_pileup_callback )
-print "##########iterator row #################"
-iter = pysam.IteratorRow( samfile, 0, 10, 200)
-for x in iter: print str(x)
-
-print "##########iterator col #################"
-iter = pysam.IteratorColumn( samfile, 0, 10, 200 )
-for x in iter: print str(x)
-
-print "#########row all##################"
-iter = pysam.IteratorRowAll( samfile )
-for x in iter: print str(x)
-
-print "###################"
+print "########### Using a callback object ###### "
class Counter:
mCounts = 0
self.mCounts += 1
c = Counter()
-samfile.fetch( "chr1:10-200", c )
+samfile.fetch( region = "chr1:10-200", callback = c )
print "counts=", c.mCounts
-sys.exit(0)
-print samfile.getTarget( 0 )
-print samfile.getTarget( 1 )
+print "########### Calling a samtools command line function ############"
-for p in pysam.pileup( "-c", "ex1.bam" ):
+for p in pysam.mpileup( "-c", "ex1.bam" ):
print str(p)
-print pysam.pileup.getMessages()
-
-for p in pysam.pileup( "-c", "ex1.bam", raw=True ):
- print str(p),
-
-
-
-print "###########################"
-
-samfile = pysam.Samfile( "ex2.sam.gz", "r" )
-
-print "num targets=", samfile.getNumTargets()
-
-iter = pysam.IteratorRowAll( samfile )
-for x in iter: print str(x)
-
-samfile.close()
-
-print "###########################"
-samfile = pysam.Samfile( "ex2.sam.gz", "r" )
-def my_fetch_callback( alignment ):
- print str(alignment)
-
-try:
- samfile.fetch( "chr1:10-20", my_fetch_callback )
-except AssertionError:
- print "caught fetch exception"
-
-samfile.close()
+print pysam.mpileup.getMessages()
-print "###########################"
-samfile = pysam.Samfile( "ex2.sam.gz", "r" )
-def my_pileup_callback( pileups ):
- print str(pileups)
-try:
- samfile.pileup( "chr1:10-20", my_pileup_callback )
-except NotImplementedError:
- print "caught pileup exception"
+print "########### Investigating headers #######################"
# playing arount with headers
samfile = pysam.Samfile( "ex3.sam", "r" )
-print samfile.targets
+print samfile.references
print samfile.lengths
print samfile.text
-print samdile.header
+print samfile.header
header = samfile.header
samfile.close()
import subprocess
import shutil
import logging
+
SAMTOOLS="samtools"
+WORKDIR="pysam_test_work"
def checkBinaryEqual( filename1, filename2 ):
'''return true if the two files are binary equal.'''
first_time = True
# a list of commands to test
- mCommands = \
- { "faidx" : \
- (
- ("ex1.fa.fai", "faidx ex1.fa"),
- ("pysam_ex1.fa.fai", (pysam.faidx, "ex1.fa") ),
- ),
- "import" :
+ commands = \
+ {
+ "view" :
(
- ("ex1.bam", "import ex1.fa.fai ex1.sam.gz ex1.bam" ),
- ("pysam_ex1.bam", (pysam.samimport, "ex1.fa.fai ex1.sam.gz pysam_ex1.bam") ),
+ ("ex1.view", "view ex1.bam > ex1.view"),
+ ("pysam_ex1.view", (pysam.view, "ex1.bam" ) ),
+ ),
+ "view2" :
+ (
+ ("ex1.view", "view -bT ex1.fa -o ex1.view2 ex1.sam"),
+ # note that -o ex1.view2 throws exception.
+ ("pysam_ex1.view", (pysam.view, "-bT ex1.fa -oex1.view2 ex1.sam" ) ),
+ ),
+ "sort" :
+ (
+ ( "ex1.sort.bam", "sort ex1.bam ex1.sort" ),
+ ( "pysam_ex1.sort.bam", (pysam.sort, "ex1.bam pysam_ex1.sort" ) ),
+ ),
+ "mpileup" :
+ (
+ ("ex1.pileup", "mpileup ex1.bam > ex1.pileup" ),
+ ("pysam_ex1.mpileup", (pysam.mpileup, "ex1.bam" ) ),
+ ),
+ "depth" :
+ (
+ ("ex1.depth", "depth ex1.bam > ex1.depth" ),
+ ("pysam_ex1.depth", (pysam.depth, "ex1.bam" ) ),
+ ),
+ "faidx" :
+ (
+ ("ex1.fa.fai", "faidx ex1.fa"),
+ ("pysam_ex1.fa.fai", (pysam.faidx, "ex1.fa") ),
),
"index":
(
("ex1.bam.bai", "index ex1.bam" ),
("pysam_ex1.bam.bai", (pysam.index, "pysam_ex1.bam" ) ),
),
- "pileup1" :
- (
- ("ex1.pileup", "pileup -cf ex1.fa ex1.bam > ex1.pileup" ),
- ("pysam_ex1.pileup", (pysam.pileup, "-c -f ex1.fa ex1.bam" ) )
+ "idxstats" :
+ (
+ ("ex1.idxstats", "idxstats ex1.bam > ex1.idxstats" ),
+ ("pysam_ex1.idxstats", (pysam.idxstats, "pysam_ex1.bam" ) ),
),
- "pileup2" :
- (
- ("ex1.glf", "pileup -gf ex1.fa ex1.bam > ex1.glf" ),
- ("pysam_ex1.glf", (pysam.pileup, "-g -f ex1.fa ex1.bam" ) )
+ "fixmate" :
+ (
+ ("ex1.fixmate", "fixmate ex1.bam ex1.fixmate" ),
+ ("pysam_ex1.fixmate", (pysam.fixmate, "pysam_ex1.bam pysam_ex1.fixmate") ),
),
- "glfview" :
- (
- ("ex1.glfview", "glfview ex1.glf > ex1.glfview"),
- ("pysam_ex1.glfview", (pysam.glfview, "ex1.glf" ) ),
+ "flagstat" :
+ (
+ ("ex1.flagstat", "flagstat ex1.bam > ex1.flagstat" ),
+ ("pysam_ex1.flagstat", (pysam.flagstat, "pysam_ex1.bam") ),
),
- "view" :
- (
- ("ex1.view", "view ex1.bam > ex1.view"),
- ("pysam_ex1.view", (pysam.view, "ex1.bam" ) ),
+ "calmd" :
+ (
+ ("ex1.calmd", "calmd ex1.bam ex1.fa > ex1.calmd" ),
+ ("pysam_ex1.calmd", (pysam.calmd, "pysam_ex1.bam ex1.fa") ),
),
- "view2" :
- (
- ("ex1.view", "view -bT ex1.fa -o ex1.view2 ex1.sam"),
- # note that -o ex1.view2 throws exception.
- ("pysam_ex1.view", (pysam.view, "-bT ex1.fa -oex1.view2 ex1.sam" ) ),
+ "merge" :
+ (
+ ("ex1.merge", "merge -f ex1.merge ex1.bam ex1.bam" ),
+ # -f option does not work - following command will cause the subsequent
+ # command to fail
+ ("pysam_ex1.merge", (pysam.merge, "pysam_ex1.merge pysam_ex1.bam pysam_ex1.bam") ),
+ ),
+ "rmdup" :
+ (
+ ("ex1.rmdup", "rmdup ex1.bam ex1.rmdup" ),
+ ("pysam_ex1.rmdup", (pysam.rmdup, "pysam_ex1.bam pysam_ex1.rmdup" )),
+ ),
+ "reheader" :
+ (
+ ( "ex1.reheader", "reheader ex1.bam ex1.bam > ex1.reheader"),
+ ( "pysam_ex1.reheader", (pysam.reheader, "ex1.bam ex1.bam" ) ),
+ ),
+ "cat":
+ (
+ ( "ex1.cat", "cat ex1.bam ex1.bam > ex1.cat"),
+ ( "pysam_ex1.cat", (pysam.cat, "ex1.bam ex1.bam" ) ),
+ ),
+ "targetcut":
+ (
+ ("ex1.targetcut", "targetcut ex1.bam > ex1.targetcut" ),
+ ("pysam_ex1.targetcut", (pysam.targetcut, "pysam_ex1.bam") ),
+ ),
+ "phase":
+ (
+ ("ex1.phase", "phase ex1.bam > ex1.phase" ),
+ ("pysam_ex1.phase", (pysam.phase, "pysam_ex1.bam") ),
+ ),
+ "import" :
+ (
+ ("ex1.bam", "import ex1.fa.fai ex1.sam.gz ex1.bam" ),
+ ("pysam_ex1.bam", (pysam.samimport, "ex1.fa.fai ex1.sam.gz pysam_ex1.bam") ),
+ ),
+ "bam2fq":
+ (
+ ("ex1.bam2fq", "bam2fq ex1.bam > ex1.bam2fq" ),
+ ("pysam_ex1.bam2fq", (pysam.bam2fq, "pysam_ex1.bam") ),
),
}
# some tests depend on others. The order specifies in which order
# the samtools commands are executed.
- mOrder = ('faidx', 'import', 'index',
- 'pileup1', 'pileup2',
+ # The first three (faidx, import, index) need to be in that order,
+ # the rest is arbitrary.
+ order = ('faidx', 'import', 'index',
+ # 'pileup1', 'pileup2', deprecated
# 'glfview', deprecated
- 'view', 'view2' )
+ 'view', 'view2',
+ 'sort',
+ 'mpileup',
+ 'depth',
+ 'idxstats',
+ 'fixmate',
+ 'flagstat',
+ # 'calmd',
+ 'merge',
+ 'rmdup',
+ 'reheader',
+ 'cat',
+ 'targetcut',
+ 'phase',
+ 'bam2fq',
+ )
def setUp( self ):
'''setup tests.
files.
'''
if BinaryTest.first_time:
- # copy the source
- shutil.copy( "ex1.fa", "pysam_ex1.fa" )
- for label in self.mOrder:
- command = self.mCommands[label]
+ # remove previous files
+ if os.path.exists( WORKDIR ):
+ shutil.rmtree( WORKDIR )
+
+ # copy the source files to WORKDIR
+ os.makedirs( WORKDIR )
+
+ shutil.copy( "ex1.fa", os.path.join( WORKDIR, "pysam_ex1.fa" ) )
+ shutil.copy( "ex1.fa", os.path.join( WORKDIR, "ex1.fa" ) )
+ shutil.copy( "ex1.sam.gz", os.path.join( WORKDIR, "ex1.sam.gz" ) )
+ shutil.copy( "ex1.sam", os.path.join( WORKDIR, "ex1.sam" ) )
+
+ # cd to workdir
+ savedir = os.getcwd()
+ os.chdir( WORKDIR )
+
+ for label in self.order:
+ command = self.commands[label]
samtools_target, samtools_command = command[0]
- pysam_target, pysam_command = command[1]
+ try:
+ pysam_target, pysam_command = command[1]
+ except ValueError, msg:
+ raise ValueError( "error while setting up %s=%s: %s" %\
+ (label, command, msg) )
runSamtools( " ".join( (SAMTOOLS, samtools_command )))
pysam_method, pysam_options = pysam_command
- output = pysam_method( *pysam_options.split(" "), raw=True)
+ try:
+ output = pysam_method( *pysam_options.split(" "), raw=True)
+ except pysam.SamtoolsError, msg:
+ raise pysam.SamtoolsError( "error while executing %s: options=%s: msg=%s" %\
+ (label, pysam_options, msg) )
if ">" in samtools_command:
outfile = open( pysam_target, "wb" )
for line in output: outfile.write( line )
outfile.close()
-
+
+ os.chdir( savedir )
BinaryTest.first_time = False
+
+
samtools_version = getSamtoolsVersion()
+
def _r( s ):
# patch - remove any of the alpha/beta suffixes, i.e., 0.1.12a -> 0.1.12
if s.count('-') > 0: s = s[0:s.find('-')]
def checkCommand( self, command ):
if command:
- samtools_target, pysam_target = self.mCommands[command][0][0], self.mCommands[command][1][0]
+ samtools_target, pysam_target = self.commands[command][0][0], self.commands[command][1][0]
+ samtools_target = os.path.join( WORKDIR, samtools_target )
+ pysam_target = os.path.join( WORKDIR, pysam_target )
self.assertTrue( checkBinaryEqual( samtools_target, pysam_target ),
"%s failed: files %s and %s are not the same" % (command, samtools_target, pysam_target) )
def testIndex( self ):
self.checkCommand( "index" )
+
+ def testSort( self ):
+ self.checkCommand( "sort" )
+
+ def testMpileup( self ):
+ self.checkCommand( "mpileup" )
+
+ def testDepth( self ):
+ self.checkCommand( "depth" )
+
+ def testIdxstats( self ):
+ self.checkCommand( "idxstats" )
+
+ def testFixmate( self ):
+ self.checkCommand( "fixmate" )
+
+ def testFlagstat( self ):
+ self.checkCommand( "flagstat" )
- def testPileup1( self ):
- self.checkCommand( "pileup1" )
+ def testMerge( self ):
+ self.checkCommand( "merge" )
+
+ def testRmdup( self ):
+ self.checkCommand( "rmdup" )
+
+ def testReheader( self ):
+ self.checkCommand( "reheader" )
+
+ def testCat( self ):
+ self.checkCommand( "cat" )
+
+ def testTargetcut( self ):
+ self.checkCommand( "targetcut" )
+
+ def testPhase( self ):
+ self.checkCommand( "phase" )
+
+ def testBam2fq( self ):
+ self.checkCommand( "bam2fq" )
+
+ # def testPileup1( self ):
+ # self.checkCommand( "pileup1" )
- def testPileup2( self ):
- self.checkCommand( "pileup2" )
+ # def testPileup2( self ):
+ # self.checkCommand( "pileup2" )
# deprecated
# def testGLFView( self ):
self.assertRaises( IOError, pysam.index, "exdoesntexist.bam" )
def __del__(self):
- return
- for label, command in self.mCommands.iteritems():
- samtools_target, samtools_command = command[0]
- pysam_target, pysam_command = command[1]
- if os.path.exists( samtools_target): os.remove( samtools_target )
- if os.path.exists( pysam_target): os.remove( pysam_target )
- if os.path.exists( "pysam_ex1.fa" ): os.remove( "pysam_ex1.fa" )
+ if os.path.exists( WORKDIR ):
+ shutil.rmtree( WORKDIR )
class IOTest(unittest.TestCase):
'''check if reading samfile and writing a samfile are consistent.'''
def checkEcho( self, input_filename, reference_filename,
output_filename,
- input_mode, output_mode, use_template = True):
+ input_mode, output_mode, use_template = True ):
'''iterate through *input_filename* writing to *output_filename* and
comparing the output to *reference_filename*.
The files are opened according to the *input_mode* and *output_mode*.
If *use_template* is set, the header is copied from infile using the
- template mechanism, otherwise target names and lengths are passed explicitely.
+ template mechanism, otherwise target names and lengths are passed
+ explicitely.
+
'''
infile = pysam.Samfile( input_filename, input_mode )
else:
outfile = pysam.Samfile( output_filename, output_mode,
referencenames = infile.references,
- referencelengths = infile.lengths )
+ referencelengths = infile.lengths,
+ add_sq_text = False )
iter = infile.fetch()
for x in iter: outfile.write( x )
self.checkEcho( input_filename, reference_filename, output_filename,
"r", "w" )
+ def testReadSamWithoutHeaderWriteSamWithoutHeader( self ):
+
+ input_filename = "ex1.sam"
+ output_filename = "pysam_ex1.sam"
+ reference_filename = "ex1.sam"
+
+ # disabled - reading from a samfile without header
+ # is not implemented.
+
+ # self.checkEcho( input_filename, reference_filename, output_filename,
+ # "r", "w" )
+
def testFetchFromClosedFile( self ):
samfile = pysam.Samfile( "ex1.bam", "rb" )
self.assertEqual( 0, samfile.write(None) )
def testAutoDetection( self ):
- samfile = pysam.Samfile( "ex3.bam" )
- samfile.fetch()
+ '''test if autodetection works.'''
+
+ samfile = pysam.Samfile( "ex3.sam" )
+ self.assertRaises( ValueError, samfile.fetch, 'chr1' )
samfile.close()
- samfile = pysam.Samfile( "ex3.sam")
- samfile.fetch()
+ samfile = pysam.Samfile( "ex3.bam" )
+ samfile.fetch('chr1')
samfile.close()
+ def testReadingFromSamFileWithoutHeader( self ):
+ '''read from samfile without header.
+ '''
+ samfile = pysam.Samfile( "ex7.sam" )
+ self.assertRaises( NotImplementedError, samfile.__iter__ )
+
def testReadingFromFileWithoutIndex( self ):
'''read from bam file without index.'''
self.assertRaises( ValueError, samfile.fetch )
self.assertEqual( len(list( samfile.fetch(until_eof = True) )), 3270 )
+ def testReadingUniversalFileMode( self ):
+ '''read from samfile without header.
+ '''
+
+ input_filename = "ex2.sam"
+ output_filename = "pysam_ex2.sam"
+ reference_filename = "ex1.sam"
+
+ self.checkEcho( input_filename, reference_filename, output_filename,
+ "rU", "w" )
+
+class TestFloatTagBug( unittest.TestCase ):
+ '''see issue 71'''
+
+ def testFloatTagBug( self ):
+ '''a float tag before another exposed a parsing bug in bam_aux_get - expected to fail
+
+ This test is expected to fail until samtools is fixed.
+ '''
+ samfile = pysam.Samfile("tag_bug.bam")
+ read = samfile.fetch(until_eof=True).next()
+ self.assertTrue( ('XC',1) in read.tags )
+ self.assertEqual(read.opt('XC'), 1)
+
+class TestTagParsing( unittest.TestCase ):
+ '''tests checking the accuracy of tag setting and retrieval.'''
+
+ def makeRead( self ):
+ a = pysam.AlignedRead()
+ a.qname = "read_12345"
+ a.tid = 0
+ a.seq="ACGT" * 3
+ a.flag = 0
+ a.rname = 0
+ a.pos = 1
+ a.mapq = 20
+ a.cigar = ( (0,10), (2,1), (0,25) )
+ a.mrnm = 0
+ a.mpos=200
+ a.isize = 0
+ a.qual ="1234" * 3
+ # todo: create tags
+ return a
+
+ def testNegativeIntegers( self ):
+ x = -2
+ aligned_read = self.makeRead()
+ aligned_read.tags = [("XD", int(x) ) ]
+ print aligned_read.tags
+
+ def testNegativeIntegers2( self ):
+ x = -2
+ r = self.makeRead()
+ r.tags = [("XD", int(x) ) ]
+ outfile = pysam.Samfile( "test.bam",
+ "wb",
+ referencenames = ("chr1",),
+ referencelengths = (1000,) )
+ outfile.write (r )
+ outfile.close()
+
class TestIteratorRow(unittest.TestCase):
def setUp(self):
def testARmrnm(self):
self.assertEqual( self.reads[0].mrnm, 0, "mate reference sequence name mismatch in read 1: %s != %s" % (self.reads[0].mrnm, 0) )
self.assertEqual( self.reads[1].mrnm, 1, "mate reference sequence name mismatch in read 2: %s != %s" % (self.reads[1].mrnm, 1) )
+ self.assertEqual( self.reads[0].rnext, 0, "mate reference sequence name mismatch in read 1: %s != %s" % (self.reads[0].rnext, 0) )
+ self.assertEqual( self.reads[1].rnext, 1, "mate reference sequence name mismatch in read 2: %s != %s" % (self.reads[1].rnext, 1) )
def testARmpos(self):
self.assertEqual( self.reads[0].mpos, 200-1, "mate mapping position mismatch in read 1: %s != %s" % (self.reads[0].mpos, 200-1) )
self.assertEqual( self.reads[1].mpos, 500-1, "mate mapping position mismatch in read 2: %s != %s" % (self.reads[1].mpos, 500-1) )
+ self.assertEqual( self.reads[0].pnext, 200-1, "mate mapping position mismatch in read 1: %s != %s" % (self.reads[0].pnext, 200-1) )
+ self.assertEqual( self.reads[1].pnext, 500-1, "mate mapping position mismatch in read 2: %s != %s" % (self.reads[1].pnext, 500-1) )
def testARisize(self):
self.assertEqual( self.reads[0].isize, 167, "insert size mismatch in read 1: %s != %s" % (self.reads[0].isize, 167) )
self.assertEqual( self.reads[1].isize, 412, "insert size mismatch in read 2: %s != %s" % (self.reads[1].isize, 412) )
+ self.assertEqual( self.reads[0].tlen, 167, "insert size mismatch in read 1: %s != %s" % (self.reads[0].tlen, 167) )
+ self.assertEqual( self.reads[1].tlen, 412, "insert size mismatch in read 2: %s != %s" % (self.reads[1].tlen, 412) )
def testARseq(self):
self.assertEqual( self.reads[0].seq, "AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG", "sequence mismatch in read 1: %s != %s" % (self.reads[0].seq, "AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG") )
self.assertRaises( ValueError, pysam.Samfile, 'ex1.sam', 'rb' )
def testOpenBamAsSam( self ):
- self.assertRaises( ValueError, pysam.Samfile, 'ex1.bam', 'r' )
+ # test fails, needs to be implemented.
+ # sam.fetch() fails on reading, not on opening
+ # self.assertRaises( ValueError, pysam.Samfile, 'ex1.bam', 'r' )
+ pass
def testOpenFastaAsSam( self ):
- self.assertRaises( ValueError, pysam.Samfile, 'ex1.fa', 'r' )
+ # test fails, needs to be implemented.
+ # sam.fetch() fails on reading, not on opening
+ # self.assertRaises( ValueError, pysam.Samfile, 'ex1.fa', 'r' )
+ pass
def testOpenFastaAsBam( self ):
self.assertRaises( ValueError, pysam.Samfile, 'ex1.fa', 'rb' )
self.assertEqual( a.rname, 0 )
self.assertEqual( a.mapq, 0 )
self.assertEqual( a.cigar, None )
- self.assertEqual( a.tags, None )
+ self.assertEqual( a.tags, [] )
self.assertEqual( a.mrnm, 0 )
self.assertEqual( a.mpos, 0 )
self.assertEqual( a.isize, 0 )
samfile = pysam.Samfile("ex10.bam", "rb")
self.check( samfile )
-class TestSNPCalls( unittest.TestCase ):
- '''test pysam SNP calling ability.'''
-
- def checkEqual( self, a, b ):
- for x in ("reference_base",
- "pos",
- "genotype",
- "consensus_quality",
- "snp_quality",
- "mapping_quality",
- "coverage" ):
- self.assertEqual( getattr(a, x), getattr(b,x), "%s mismatch: %s != %s\n%s\n%s" %
- (x, getattr(a, x), getattr(b,x), str(a), str(b)))
-
- def testAllPositionsViaIterator( self ):
- samfile = pysam.Samfile( "ex1.bam", "rb")
- fastafile = pysam.Fastafile( "ex1.fa" )
- try:
- refs = [ x for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ) if x.reference_base != "*"]
- except pysam.SamtoolsError:
- pass
-
- i = samfile.pileup( stepper = "samtools", fastafile = fastafile )
- calls = list(pysam.IteratorSNPCalls(i))
- for x,y in zip( refs, calls ):
- self.checkEqual( x, y )
-
- def testPerPositionViaIterator( self ):
- # test pileup for each position. This is a slow operation
- # so this test is disabled
- return
- samfile = pysam.Samfile( "ex1.bam", "rb")
- fastafile = pysam.Fastafile( "ex1.fa" )
- for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ):
- if x.reference_base == "*": continue
- i = samfile.pileup( x.chromosome, x.pos, x.pos+1,
- fastafile = fastafile,
- stepper = "samtools" )
- z = [ zz for zz in pysam.IteratorSamtools(i) if zz.pos == x.pos ]
- self.assertEqual( len(z), 1 )
- self.checkEqual( x, z[0] )
-
- def testPerPositionViaCaller( self ):
- # test pileup for each position. This is a fast operation
- samfile = pysam.Samfile( "ex1.bam", "rb")
- fastafile = pysam.Fastafile( "ex1.fa" )
- i = samfile.pileup( stepper = "samtools", fastafile = fastafile )
- caller = pysam.SNPCaller( i )
-
- for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ):
- if x.reference_base == "*": continue
- call = caller.call( x.chromosome, x.pos )
- self.checkEqual( x, call )
-
-class TestIndelCalls( unittest.TestCase ):
- '''test pysam indel calling.'''
-
- def checkEqual( self, a, b ):
-
- for x in ("pos",
- "genotype",
- "consensus_quality",
- "snp_quality",
- "mapping_quality",
- "coverage",
- "first_allele",
- "second_allele",
- "reads_first",
- "reads_second",
- "reads_diff"):
- if b.genotype == "*/*" and x == "second_allele":
- # ignore test for second allele (positions chr2:439 and chr2:1512)
- continue
- self.assertEqual( getattr(a, x), getattr(b,x), "%s mismatch: %s != %s\n%s\n%s" %
- (x, getattr(a, x), getattr(b,x), str(a), str(b)))
-
- def testAllPositionsViaIterator( self ):
-
- samfile = pysam.Samfile( "ex1.bam", "rb")
- fastafile = pysam.Fastafile( "ex1.fa" )
- try:
- refs = [ x for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ) if x.reference_base == "*"]
- except pysam.SamtoolsError:
- pass
-
- i = samfile.pileup( stepper = "samtools", fastafile = fastafile )
- calls = [ x for x in list(pysam.IteratorIndelCalls(i)) if x != None ]
- for x,y in zip( refs, calls ):
- self.checkEqual( x, y )
-
- def testPerPositionViaCaller( self ):
- # test pileup for each position. This is a fast operation
- samfile = pysam.Samfile( "ex1.bam", "rb")
- fastafile = pysam.Fastafile( "ex1.fa" )
- i = samfile.pileup( stepper = "samtools", fastafile = fastafile )
- caller = pysam.IndelCaller( i )
-
- for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ):
- if x.reference_base != "*": continue
- call = caller.call( x.chromosome, x.pos )
- self.checkEqual( x, call )
+# class TestSNPCalls( unittest.TestCase ):
+# '''test pysam SNP calling ability.'''
+
+# def checkEqual( self, a, b ):
+# for x in ("reference_base",
+# "pos",
+# "genotype",
+# "consensus_quality",
+# "snp_quality",
+# "mapping_quality",
+# "coverage" ):
+# self.assertEqual( getattr(a, x), getattr(b,x), "%s mismatch: %s != %s\n%s\n%s" %
+# (x, getattr(a, x), getattr(b,x), str(a), str(b)))
+
+# def testAllPositionsViaIterator( self ):
+# samfile = pysam.Samfile( "ex1.bam", "rb")
+# fastafile = pysam.Fastafile( "ex1.fa" )
+# try:
+# refs = [ x for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ) if x.reference_base != "*"]
+# except pysam.SamtoolsError:
+# pass
+
+# i = samfile.pileup( stepper = "samtools", fastafile = fastafile )
+# calls = list(pysam.IteratorSNPCalls(i))
+# for x,y in zip( refs, calls ):
+# self.checkEqual( x, y )
+
+# def testPerPositionViaIterator( self ):
+# # test pileup for each position. This is a slow operation
+# # so this test is disabled
+# return
+# samfile = pysam.Samfile( "ex1.bam", "rb")
+# fastafile = pysam.Fastafile( "ex1.fa" )
+# for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ):
+# if x.reference_base == "*": continue
+# i = samfile.pileup( x.chromosome, x.pos, x.pos+1,
+# fastafile = fastafile,
+# stepper = "samtools" )
+# z = [ zz for zz in pysam.IteratorSamtools(i) if zz.pos == x.pos ]
+# self.assertEqual( len(z), 1 )
+# self.checkEqual( x, z[0] )
+
+# def testPerPositionViaCaller( self ):
+# # test pileup for each position. This is a fast operation
+# samfile = pysam.Samfile( "ex1.bam", "rb")
+# fastafile = pysam.Fastafile( "ex1.fa" )
+# i = samfile.pileup( stepper = "samtools", fastafile = fastafile )
+# caller = pysam.SNPCaller( i )
+
+# for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ):
+# if x.reference_base == "*": continue
+# call = caller.call( x.chromosome, x.pos )
+# self.checkEqual( x, call )
+
+# class TestIndelCalls( unittest.TestCase ):
+# '''test pysam indel calling.'''
+
+# def checkEqual( self, a, b ):
+
+# for x in ("pos",
+# "genotype",
+# "consensus_quality",
+# "snp_quality",
+# "mapping_quality",
+# "coverage",
+# "first_allele",
+# "second_allele",
+# "reads_first",
+# "reads_second",
+# "reads_diff"):
+# if b.genotype == "*/*" and x == "second_allele":
+# # ignore test for second allele (positions chr2:439 and chr2:1512)
+# continue
+# self.assertEqual( getattr(a, x), getattr(b,x), "%s mismatch: %s != %s\n%s\n%s" %
+# (x, getattr(a, x), getattr(b,x), str(a), str(b)))
+
+# def testAllPositionsViaIterator( self ):
+
+# samfile = pysam.Samfile( "ex1.bam", "rb")
+# fastafile = pysam.Fastafile( "ex1.fa" )
+# try:
+# refs = [ x for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ) if x.reference_base == "*"]
+# except pysam.SamtoolsError:
+# pass
+
+# i = samfile.pileup( stepper = "samtools", fastafile = fastafile )
+# calls = [ x for x in list(pysam.IteratorIndelCalls(i)) if x != None ]
+# for x,y in zip( refs, calls ):
+# self.checkEqual( x, y )
+
+# def testPerPositionViaCaller( self ):
+# # test pileup for each position. This is a fast operation
+# samfile = pysam.Samfile( "ex1.bam", "rb")
+# fastafile = pysam.Fastafile( "ex1.fa" )
+# i = samfile.pileup( stepper = "samtools", fastafile = fastafile )
+# caller = pysam.IndelCaller( i )
+
+# for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ):
+# if x.reference_base != "*": continue
+# call = caller.call( x.chromosome, x.pos )
+# self.checkEqual( x, call )
class TestLogging( unittest.TestCase ):
'''test around bug issue 42,
self.assertEqual( read.pos, mate.mpos )
self.assertEqual( read.mpos, mate.pos )
+ def testIndexStats( self ):
+ '''test if total number of mapped/unmapped reads is correct.'''
+
+ samfile = pysam.Samfile( "ex1.bam", "rb" )
+ self.assertEqual( samfile.mapped, 3235 )
+ self.assertEqual( samfile.unmapped, 35 )
+
class TestSamtoolsProxy( unittest.TestCase ):
'''tests for sanity checking access to samtools functions.'''
b.difference(a) ))
for x, d in enumerate( zip( result, ref )):
-
self.assertEqual( d[0], d[1],
"unexpected results in pair %i: '%s', expected '%s'" % \
(x,
header = list( self.tabix.header )
self.assertEqual( ref, header )
+ def testReopening( self ):
+ '''test repeated opening of the same file.'''
+ def func1():
+ # opens any tabix file
+ inf = pysam.Tabixfile(self.filename)
+ return
+
+ for i in range(10000):
+ func1()
+
+
class TestParser( unittest.TestCase ):
filename = "example.gtf.gz"
self.assertEqual( self.compare[x], list(r) )
self.assertEqual( len(self.compare[x]), len(r) )
+ # test indexing
for c in range(0,len(r)):
self.assertEqual( self.compare[x][c], r[c] )
+ # test slicing access
+ for c in range(0, len(r)-1):
+ for cc in range(c+1, len(r)):
+ self.assertEqual( self.compare[x][c:cc],
+ r[c:cc] )
+
def testWrite( self ):
for x, r in enumerate(self.tabix.fetch( parser = pysam.asTuple() )):
self.assertEqual( "\t".join(e), str(r) )
class TestGTF( TestParser ):
+
def testRead( self ):
for x, r in enumerate(self.tabix.fetch( parser = pysam.asGTF() )):
- self.assertEqual( "\t".join( self.compare[x]), str(r) )
+ c = self.compare[x]
+
+ self.assertEqual( len(c), len(r) )
+ self.assertEqual( "\t".join(c), str(r) )
+ self.assertTrue( r.gene_id.startswith("ENSG") )
+ if r.feature != "gene":
+ self.assertTrue( r.transcript_id.startswith("ENST") )
+ self.assertEqual( c[0], r.contig )
class TestBed( unittest.TestCase ):
filename = "example.bed.gz"
c = self.compare[x]
for y, field in enumerate( self.columns ):
if field == "pos":
- self.assertEqual( int(c[y])-1, getattr( r, field ) )
- self.assertEqual( int(c[y])-1, r.pos )
+ self.assertEqual( int(c[y]) - 1, getattr( r, field ) )
+ self.assertEqual( int(c[y]) - 1, r.pos )
else:
self.assertEqual( c[y], getattr( r, field ),
"mismatch in field %s: %s != %s" %\
ncolumns = len(self.columns)
for x, r in enumerate(self.tabix.fetch( parser = pysam.asVCF() )):
+
c = self.compare[x]
+
+ # check unmodified string
+ ref_string = "\t".join( c )
+ cmp_string = str(r)
+ self.assertEqual( ref_string, cmp_string )
+
+ # set fields and compare field-wise
for y, field in enumerate( self.columns ):
if field == "pos":
- r.pos += 1
- self.assertEqual( int(c[y]), getattr( r, field ) )
- self.assertEqual( int(c[y]), r.pos )
+ rpos = getattr( r, field )
+ self.assertEqual( int(c[y]) - 1, rpos )
+ self.assertEqual( int(c[y]) - 1, r.pos )
+ # increment pos by 1
+ setattr( r, field, rpos + 1 )
+ self.assertEqual( getattr( r, field ), rpos + 1 )
+ c[y] = str(int(c[y]) + 1 )
else:
setattr( r, field, "test_%i" % y)
c[y] = "test_%i" % y
c[ncolumns+y] = "test_%i" % y
r[y] = "test_%i" % y
self.assertEqual( c[ncolumns+y], r[y] )
+
+class TestVCF( TestParser ):
+
+ filename = "example.vcf40.gz"
+
+ def testOpening( self ):
+ while 1:
+ infile = pysam.Tabixfile( self.filename )
+ infile.close()
+
+ # check strings
+ ref_string = "\t".join( c )
+ cmp_string = str(r)
+
+ self.assertEqual( ref_string, cmp_string )
+
if __name__ == "__main__":
unittest.main()
projects / pysam.git / commitdiff