Imported Upstream version 0.5

[pysam.git] / pysam / cvcf.c

diff --git a/pysam/cvcf.c b/pysam/cvcf.c
index d194519d5e20e227a6c1d69ba9d9128e3f26b897..82eae7d1868ff4b1072995053ff6b22929a2d1c7 100644 (file)
--- a/pysam/cvcf.c
+++ b/pysam/cvcf.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.14.1 on Sat Oct 15 05:27:48 2011 */
+/* Generated by Cython 0.13 on Thu May  5 15:40:49 2011 */
 
 #define PY_SSIZE_T_CLEAN
 #include "Python.h"
@@ -126,20 +126,15 @@
   #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)
@@ -156,7 +151,7 @@
 #endif
 
 #if PY_MAJOR_VERSION >= 3
-  #define PyBoolObject                 PyLongObject
+  #define PyBoolObject PyLongObject
 #endif
 
 
@@ -168,25 +163,6 @@
   #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
@@ -232,11 +208,6 @@
 #include "bgzf.h"
 #include "tabix.h"
 
-#ifdef PYREX_WITHOUT_ASSERTIONS
-#define CYTHON_WITHOUT_ASSERTIONS
-#endif
-
-
 /* inline attribute */
 #ifndef CYTHON_INLINE
   #if defined(__GNUC__)
@@ -246,7 +217,7 @@
   #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
     #define CYTHON_INLINE inline
   #else
-    #define CYTHON_INLINE
+    #define CYTHON_INLINE 
   #endif
 #endif
 
@@ -254,14 +225,14 @@
 #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
 
@@ -286,7 +257,7 @@ static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
 
 #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 ... */
@@ -316,7 +287,7 @@ static const char *__pyx_f[] = {
 
 /* Type declarations */
 
-/* "TabProxies.pxd":42
+/* "pysam/TabProxies.pxd":42
  *   ctypedef int uint64_t
  * 
  * cdef class TupleProxy:             # <<<<<<<<<<<<<<
@@ -336,7 +307,7 @@ struct __pyx_obj_10TabProxies_TupleProxy {
   int is_modified;
 };
 
-/* "TabProxies.pxd":77
+/* "pysam/TabProxies.pxd":77
  *     cdef update( self, char * buffer, size_t nbytes )
  * 
  * cdef class NamedTupleProxy( TupleProxy) :             # <<<<<<<<<<<<<<
@@ -348,7 +319,7 @@ struct __pyx_obj_10TabProxies_NamedTupleProxy {
   struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
 };
 
-/* "TabProxies.pxd":80
+/* "pysam/TabProxies.pxd":80
  *     pass
  * 
  * cdef class BedProxy( NamedTupleProxy) :             # <<<<<<<<<<<<<<
@@ -364,7 +335,7 @@ struct __pyx_obj_10TabProxies_BedProxy {
   int bedfields;
 };
 
-/* "cvcf.pyx":94
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94
  * ###########################################################################################################
  * 
  * cdef class VCFRecord( TabProxies.TupleProxy):             # <<<<<<<<<<<<<<
@@ -379,7 +350,7 @@ struct __pyx_obj_4cvcf_VCFRecord {
   uint32_t pos;
 };
 
-/* "TabProxies.pxd":91
+/* "pysam/TabProxies.pxd":91
  *     cdef update( self, char * buffer, size_t nbytes )
  * 
  * cdef class VCFProxy( NamedTupleProxy) :             # <<<<<<<<<<<<<<
@@ -393,7 +364,7 @@ struct __pyx_obj_10TabProxies_VCFProxy {
   uint32_t pos;
 };
 
-/* "ctabix.pxd":178
+/* "pysam/ctabix.pxd":178
  *     cdef tabix_t * tabixfile
  * 
  * cdef class Parser:             # <<<<<<<<<<<<<<
@@ -404,7 +375,7 @@ struct __pyx_obj_6ctabix_Parser {
   PyObject_HEAD
 };
 
-/* "TabProxies.pxd":60
+/* "pysam/TabProxies.pxd":60
  *     cdef update( self, char * buffer, size_t nbytes )
  * 
  * cdef class GTFProxy( TupleProxy) :             # <<<<<<<<<<<<<<
@@ -426,7 +397,7 @@ struct __pyx_obj_10TabProxies_GTFProxy {
   int hasOwnAttributes;
 };
 
-/* "cvcf.pyx":221
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":221
  * 
  * 
  * cdef class asVCFRecord( ctabix.Parser ):             # <<<<<<<<<<<<<<
@@ -439,7 +410,7 @@ struct __pyx_obj_4cvcf_asVCFRecord {
   PyObject *vcffile;
 };
 
-/* "ctabix.pxd":172
+/* "pysam/ctabix.pxd":172
  *   # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
  * 
  * cdef class Tabixfile:             # <<<<<<<<<<<<<<
@@ -454,7 +425,7 @@ struct __pyx_obj_6ctabix_Tabixfile {
 };
 
 
-/* "TabProxies.pxd":42
+/* "pysam/TabProxies.pxd":42
  *   ctypedef int uint64_t
  * 
  * cdef class TupleProxy:             # <<<<<<<<<<<<<<
@@ -472,7 +443,7 @@ struct __pyx_vtabstruct_10TabProxies_TupleProxy {
 static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
 
 
-/* "TabProxies.pxd":77
+/* "pysam/TabProxies.pxd":77
  *     cdef update( self, char * buffer, size_t nbytes )
  * 
  * cdef class NamedTupleProxy( TupleProxy) :             # <<<<<<<<<<<<<<
@@ -486,7 +457,7 @@ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy {
 static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
 
 
-/* "TabProxies.pxd":91
+/* "pysam/TabProxies.pxd":91
  *     cdef update( self, char * buffer, size_t nbytes )
  * 
  * cdef class VCFProxy( NamedTupleProxy) :             # <<<<<<<<<<<<<<
@@ -500,7 +471,7 @@ struct __pyx_vtabstruct_10TabProxies_VCFProxy {
 static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
 
 
-/* "TabProxies.pxd":60
+/* "pysam/TabProxies.pxd":60
  *     cdef update( self, char * buffer, size_t nbytes )
  * 
  * cdef class GTFProxy( TupleProxy) :             # <<<<<<<<<<<<<<
@@ -514,7 +485,7 @@ struct __pyx_vtabstruct_10TabProxies_GTFProxy {
 static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
 
 
-/* "cvcf.pyx":94
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94
  * ###########################################################################################################
  * 
  * cdef class VCFRecord( TabProxies.TupleProxy):             # <<<<<<<<<<<<<<
@@ -528,7 +499,7 @@ struct __pyx_vtabstruct_4cvcf_VCFRecord {
 static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord;
 
 
-/* "TabProxies.pxd":80
+/* "pysam/TabProxies.pxd":80
  *     pass
  * 
  * cdef class BedProxy( NamedTupleProxy) :             # <<<<<<<<<<<<<<
@@ -589,12 +560,12 @@ static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies
 
 static PyObject *__Pyx_GetName(PyObject *dict, PyObject *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 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*/
 
 
@@ -673,11 +644,6 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i)
 
 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) \
@@ -686,6 +652,7 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
 
 static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
 
+
 #if PY_MAJOR_VERSION >= 3
 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
     PyObject *value;
@@ -856,24 +823,12 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb);
 
 static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
 
-static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/
-
-static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
-                                   PyObject *modname); /*proto*/
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, const char *modname); /*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 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 int __pyx_binding_PyCFunctionType_init(void); /* proto */
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
 
 static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
 
@@ -913,7 +868,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
 
 static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
 
-static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
+static int __Pyx_GetVtable(PyObject *dict, void *vtabptr); /*proto*/
 
 static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
 
@@ -936,7 +891,7 @@ static PyTypeObject *__pyx_ptype_10TabProxies_VCFProxy = 0;
 static PyTypeObject *__pyx_ptype_4cvcf_VCFRecord = 0;
 static PyTypeObject *__pyx_ptype_4cvcf_asVCFRecord = 0;
 #define __Pyx_MODULE_NAME "cvcf"
-static int __pyx_module_is_main_cvcf = 0;
+int __pyx_module_is_main_cvcf = 0;
 
 /* Implementation of cvcf */
 static PyObject *__pyx_builtin_object;
@@ -952,108 +907,126 @@ static PyObject *__pyx_builtin_KeyError;
 static PyObject *__pyx_builtin_NotImplementedError;
 static char __pyx_k_1[] = "";
 static char __pyx_k_2[] = ",";
-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_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__0[] = "0";
 static char __pyx_k__D[] = "D";
 static char __pyx_k__I[] = "I";
 static char __pyx_k__N[] = "N";
-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_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__DP[] = "DP";
 static char __pyx_k__FT[] = "FT";
 static char __pyx_k__GQ[] = "GQ";
@@ -1090,7 +1063,6 @@ static char __pyx_k__Type[] = "Type";
 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";
@@ -1133,7 +1105,6 @@ static char __pyx_k__Number[] = "Number";
 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";
@@ -1251,7 +1222,6 @@ static char __pyx_k__convertGTback[] = "convertGTback";
 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";
@@ -1273,107 +1243,124 @@ static char __pyx_k__NT_PHASED_GENOTYPES[] = "NT_PHASED_GENOTYPES";
 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_n_s_101;
+static PyObject *__pyx_kp_s_10;
+static PyObject *__pyx_kp_s_100;
+static PyObject *__pyx_kp_s_101;
 static PyObject *__pyx_kp_s_102;
 static PyObject *__pyx_kp_s_103;
-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_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_14;
-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_16;
+static PyObject *__pyx_n_s_17;
+static PyObject *__pyx_kp_s_18;
 static PyObject *__pyx_kp_s_19;
 static PyObject *__pyx_kp_s_2;
 static PyObject *__pyx_n_s_20;
-static PyObject *__pyx_kp_s_21;
+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_25;
+static PyObject *__pyx_n_s_26;
 static PyObject *__pyx_kp_s_27;
-static PyObject *__pyx_n_s_29;
+static PyObject *__pyx_kp_s_28;
+static PyObject *__pyx_kp_s_29;
+static PyObject *__pyx_kp_s_3;
 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_n_s_38;
-static PyObject *__pyx_n_s_39;
+static PyObject *__pyx_kp_s_35;
+static PyObject *__pyx_kp_s_38;
+static PyObject *__pyx_kp_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_55;
+static PyObject *__pyx_kp_s_53;
+static PyObject *__pyx_kp_s_54;
+static PyObject *__pyx_n_s_55;
 static PyObject *__pyx_kp_s_56;
 static PyObject *__pyx_kp_s_57;
-static PyObject *__pyx_kp_s_58;
-static PyObject *__pyx_kp_s_59;
+static PyObject *__pyx_n_s_58;
+static PyObject *__pyx_n_s_59;
+static PyObject *__pyx_kp_b_6;
 static PyObject *__pyx_kp_s_6;
-static PyObject *__pyx_kp_s_61;
-static PyObject *__pyx_kp_s_62;
+static PyObject *__pyx_n_s_60;
+static PyObject *__pyx_n_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_kp_s_69;
+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_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_n_s_79;
+static PyObject *__pyx_kp_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_n_s_87;
+static PyObject *__pyx_kp_s_86;
+static PyObject *__pyx_kp_s_87;
 static PyObject *__pyx_kp_s_88;
 static PyObject *__pyx_kp_s_89;
-static PyObject *__pyx_kp_b_9;
-static PyObject *__pyx_kp_s_9;
-static PyObject *__pyx_n_s_90;
+static PyObject *__pyx_n_s_9;
+static PyObject *__pyx_kp_s_90;
 static PyObject *__pyx_kp_s_91;
 static PyObject *__pyx_kp_s_92;
-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_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_kp_s__0;
 static PyObject *__pyx_n_s__ACGTN;
 static PyObject *__pyx_n_s__ALT;
@@ -1415,7 +1402,6 @@ static PyObject *__pyx_n_s__NT_PHASED_GENOTYPES;
 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;
@@ -1468,7 +1454,6 @@ static PyObject *__pyx_n_s__alleleRegEx;
 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;
@@ -1480,7 +1465,6 @@ static PyObject *__pyx_n_s__contig;
 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;
@@ -1547,7 +1531,6 @@ static PyObject *__pyx_n_s__parse_format;
 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;
@@ -1633,70 +1616,14 @@ static PyObject *__pyx_int_33;
 static PyObject *__pyx_int_40;
 static PyObject *__pyx_int_100;
 static PyObject *__pyx_int_3000000000;
-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;
-static PyObject *__pyx_k_tuple_109;
-static PyObject *__pyx_k_tuple_110;
-static PyObject *__pyx_k_tuple_114;
-static PyObject *__pyx_k_tuple_116;
-static PyObject *__pyx_k_tuple_117;
-static PyObject *__pyx_k_tuple_120;
-static PyObject *__pyx_k_tuple_123;
-static PyObject *__pyx_k_tuple_124;
-static PyObject *__pyx_k_tuple_125;
-static PyObject *__pyx_k_tuple_127;
-static PyObject *__pyx_k_tuple_129;
-static PyObject *__pyx_k_tuple_131;
-
-/* "cvcf.pyx":58
+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
  * 
  * # Utility function.  Uses 0-based coordinates
  * def get_sequence(chrom, start, end, fa):             # <<<<<<<<<<<<<<
@@ -1705,7 +1632,6 @@ static PyObject *__pyx_k_tuple_131;
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 static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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 static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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   PyObject *__pyx_v_start = 0;
@@ -1783,7 +1709,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p
   __pyx_L4_argument_unpacking_done:;
   __pyx_v_sequence = Py_None; __Pyx_INCREF(Py_None);
 
-  /* "cvcf.pyx":60
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":60
  * def get_sequence(chrom, start, end, fa):
  *     # obtain sequence from .fa file, without truncation
  *     if end<=start: return ""             # <<<<<<<<<<<<<<
@@ -1803,7 +1729,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p
   }
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-  /* "cvcf.pyx":61
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":61
  *     # obtain sequence from .fa file, without truncation
  *     if end<=start: return ""
  *     if not fa: return "N"*(end-start)             # <<<<<<<<<<<<<<
@@ -1826,7 +1752,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p
   }
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-  /* "cvcf.pyx":62
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":62
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@@ -1847,7 +1773,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p
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-    __Pyx_GOTREF(((PyObject *)__pyx_t_5));
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+    __pyx_t_6 = PyObject_Call(__pyx_t_4, __pyx_t_5, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
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   }
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-  /* "cvcf.pyx":63
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":63
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  *     if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
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@@ -1891,7 +1817,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+  __Pyx_GOTREF(__pyx_t_6);
   __Pyx_INCREF(__pyx_v_chrom);
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   __Pyx_GIVEREF(__pyx_v_chrom);
@@ -1901,10 +1827,10 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p
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-  __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(__pyx_t_5, __pyx_t_6, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
   __pyx_t_6 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__upper); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -1915,7 +1841,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p
   __pyx_v_sequence = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "cvcf.pyx":64
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":64
  *     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))             # <<<<<<<<<<<<<<
@@ -1956,7 +1882,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p
   }
   __pyx_L9:;
 
-  /* "cvcf.pyx":65
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":65
  *     sequence = fa.fetch(chrom, start, end).upper()
  *     if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
  *     return sequence             # <<<<<<<<<<<<<<
@@ -1984,7 +1910,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p
   return __pyx_r;
 }
 
-/* "cvcf.pyx":68
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":68
  * 
  * # Utility function.  Parses a region string
  * def parse_regions( string ):             # <<<<<<<<<<<<<<
@@ -1992,9 +1918,8 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p
  *     for r in string.split(','):
  */
 
-static PyObject *__pyx_pf_4cvcf_1parse_regions(PyObject *__pyx_self, PyObject *__pyx_v_string); /*proto*/
-static PyMethodDef __pyx_mdef_4cvcf_1parse_regions = {__Pyx_NAMESTR("parse_regions"), (PyCFunction)__pyx_pf_4cvcf_1parse_regions, METH_O, __Pyx_DOCSTR(0)};
-static PyObject *__pyx_pf_4cvcf_1parse_regions(PyObject *__pyx_self, PyObject *__pyx_v_string) {
+static PyObject *__pyx_pf_4cvcf_parse_regions(PyObject *__pyx_self, PyObject *__pyx_v_string); /*proto*/
+static PyObject *__pyx_pf_4cvcf_parse_regions(PyObject *__pyx_self, PyObject *__pyx_v_string) {
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   PyObject *__pyx_v_r;
   PyObject *__pyx_v_elts;
@@ -2015,7 +1940,7 @@ static PyObject *__pyx_pf_4cvcf_1parse_regions(PyObject *__pyx_self, PyObject *_
   int __pyx_t_10;
   __Pyx_RefNannySetupContext("parse_regions");
   __pyx_self = __pyx_self;
-  __pyx_v_result = ((PyObject*)Py_None); __Pyx_INCREF(Py_None);
+  __pyx_v_result = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
   __pyx_v_r = Py_None; __Pyx_INCREF(Py_None);
   __pyx_v_elts = Py_None; __Pyx_INCREF(Py_None);
   __pyx_v_chrom = Py_None; __Pyx_INCREF(Py_None);
@@ -2023,7 +1948,7 @@ static PyObject *__pyx_pf_4cvcf_1parse_regions(PyObject *__pyx_self, PyObject *_
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   __pyx_v_ielts = Py_None; __Pyx_INCREF(Py_None);
 
-  /* "cvcf.pyx":69
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":69
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  * def parse_regions( string ):
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@@ -2036,7 +1961,7 @@ static PyObject *__pyx_pf_4cvcf_1parse_regions(PyObject *__pyx_self, PyObject *_
   __pyx_v_result = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "cvcf.pyx":70
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":70
  * def parse_regions( string ):
  *     result = []
  *     for r in string.split(','):             # <<<<<<<<<<<<<<
@@ -2045,75 +1970,87 @@ static PyObject *__pyx_pf_4cvcf_1parse_regions(PyObject *__pyx_self, PyObject *_
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-      __pyx_t_3 = PyIter_Next(__pyx_t_1);
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-    /* "cvcf.pyx":71
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-    /* "cvcf.pyx":73
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-    /* "cvcf.pyx":74
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+        __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
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         __Pyx_GOTREF(__pyx_t_5);
-        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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-          __Pyx_GOTREF(((PyObject *)__pyx_t_3));
-          PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_5));
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-          __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
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-            __Pyx_GOTREF(((PyObject *)__pyx_t_3));
-            PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_5);
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-            __Pyx_GOTREF(__pyx_t_3);
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-            PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
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-            __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
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-          /* "cvcf.pyx":79
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-            __Pyx_GOTREF(((PyObject *)__pyx_t_9));
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-            __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
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-            __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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-      /* "cvcf.pyx":81
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+      __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_5), __pyx_v_r); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+      __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
-      __Pyx_Raise(__pyx_t_4, 0, 0);
+      PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_1));
+      __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+      __pyx_t_1 = 0;
+      __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __Pyx_GOTREF(__pyx_t_1);
       __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+      __Pyx_Raise(__pyx_t_1, 0, 0);
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-  PyObject *__pyx_t_5 = NULL;
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-    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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-      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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-      /* "cvcf.pyx":343
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-    /* "cvcf.pyx":344
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+    __pyx_t_2 = PySequence_GetSlice(__pyx_v_format, 1, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "cvcf.pyx":345
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-  /* "cvcf.pyx":346
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-  /* "cvcf.pyx":347
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-    /* "cvcf.pyx":348
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-      __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
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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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-    __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
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-    /* "cvcf.pyx":413
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@@ -6975,15 +7053,15 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje
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-    __Pyx_GOTREF(((PyObject *)__pyx_t_6));
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-      __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
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-    __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+    __Pyx_GOTREF(__pyx_t_2);
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+    __pyx_t_6 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+    __pyx_t_2 = PyNumber_Add(((PyObject *)__pyx_kp_s_16), __pyx_t_6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_6 = PyNumber_Add(__pyx_t_2, ((PyObject *)__pyx_kp_s_18)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -7074,7 +7153,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje
   }
   __pyx_L8:;
 
-  /* "cvcf.pyx":416
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":416
  *         else:
  *             format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">"
  *         return format             # <<<<<<<<<<<<<<
@@ -7109,7 +7188,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje
   return __pyx_r;
 }
 
-/* "cvcf.pyx":418
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":418
  *         return format
  * 
  *     def get_expected(self, format, formatdict, alt):             # <<<<<<<<<<<<<<
@@ -7117,9 +7196,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje
  *         if fmt.numbertype == self.NT_UNKNOWN: return -1
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_4get_expected = {__Pyx_NAMESTR("get_expected"), (PyCFunction)__pyx_pf_4cvcf_3VCF_4get_expected, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
-static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_get_expected(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_get_expected = {__Pyx_NAMESTR("get_expected"), (PyCFunction)__pyx_pf_4cvcf_3VCF_get_expected, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pf_4cvcf_3VCF_get_expected(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_format = 0;
   PyObject *__pyx_v_formatdict = 0;
@@ -7195,7 +7274,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec
   __pyx_L4_argument_unpacking_done:;
   __pyx_v_fmt = Py_None; __Pyx_INCREF(Py_None);
 
-  /* "cvcf.pyx":419
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":419
  * 
  *     def get_expected(self, format, formatdict, alt):
  *         fmt = formatdict[format]             # <<<<<<<<<<<<<<
@@ -7208,7 +7287,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec
   __pyx_v_fmt = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "cvcf.pyx":420
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":420
  *     def get_expected(self, format, formatdict, alt):
  *         fmt = formatdict[format]
  *         if fmt.numbertype == self.NT_UNKNOWN: return -1             # <<<<<<<<<<<<<<
@@ -7234,7 +7313,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec
   }
   __pyx_L6:;
 
-  /* "cvcf.pyx":421
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":421
  *         fmt = formatdict[format]
  *         if fmt.numbertype == self.NT_UNKNOWN: return -1
  *         if fmt.numbertype == self.NT_NUMBER: return fmt.number             # <<<<<<<<<<<<<<
@@ -7262,7 +7341,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec
   }
   __pyx_L7:;
 
-  /* "cvcf.pyx":422
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":422
  *         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             # <<<<<<<<<<<<<<
@@ -7291,7 +7370,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec
   }
   __pyx_L8:;
 
-  /* "cvcf.pyx":423
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":423
  *         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)             # <<<<<<<<<<<<<<
@@ -7320,7 +7399,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec
   }
   __pyx_L9:;
 
-  /* "cvcf.pyx":424
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":424
  *         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             # <<<<<<<<<<<<<<
@@ -7350,7 +7429,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec
   }
   __pyx_L10:;
 
-  /* "cvcf.pyx":425
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":425
  *         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)             # <<<<<<<<<<<<<<
@@ -7380,7 +7459,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec
   }
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-  /* "cvcf.pyx":426
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":426
  *         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)
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@@ -7407,7 +7486,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec
   return __pyx_r;
 }
 
-/* "cvcf.pyx":429
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":429
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  * 
  *     def _add_definition(self, formatdict, key, data, line ):             # <<<<<<<<<<<<<<
@@ -7415,9 +7494,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec
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  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_5_add_definition = {__Pyx_NAMESTR("_add_definition"), (PyCFunction)__pyx_pf_4cvcf_3VCF_5_add_definition, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
-static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF__add_definition(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_4cvcf_3VCF__add_definition = {__Pyx_NAMESTR("_add_definition"), (PyCFunction)__pyx_pf_4cvcf_3VCF__add_definition, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pf_4cvcf_3VCF__add_definition(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_formatdict = 0;
   PyObject *__pyx_v_key = 0;
@@ -7500,7 +7579,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
   __pyx_L4_argument_unpacking_done:;
   __Pyx_INCREF(__pyx_v_data);
 
-  /* "cvcf.pyx":430
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":430
  * 
  *     def _add_definition(self, formatdict, key, data, line ):
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@@ -7516,7 +7595,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
   }
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-  /* "cvcf.pyx":431
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":431
  *     def _add_definition(self, formatdict, key, data, line ):
  *         if key in formatdict: return
  *         self.error(line,self.ERROR_UNKNOWN_KEY,key)             # <<<<<<<<<<<<<<
@@ -7528,7 +7607,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+  __Pyx_GOTREF(__pyx_t_4);
   __Pyx_INCREF(__pyx_v_line);
   PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_line);
   __Pyx_GIVEREF(__pyx_v_line);
@@ -7538,13 +7617,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
   PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_key);
   __Pyx_GIVEREF(__pyx_v_key);
   __pyx_t_3 = 0;
-  __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(__pyx_t_2, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+  __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "cvcf.pyx":432
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":432
  *         if key in formatdict: return
  *         self.error(line,self.ERROR_UNKNOWN_KEY,key)
  *         if data == None:             # <<<<<<<<<<<<<<
@@ -7557,7 +7636,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
   if (__pyx_t_1) {
 
-    /* "cvcf.pyx":433
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":433
  *         self.error(line,self.ERROR_UNKNOWN_KEY,key)
  *         if data == None:
  *             formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")             # <<<<<<<<<<<<<<
@@ -7569,7 +7648,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
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-    __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+    __Pyx_GOTREF(__pyx_t_2);
     __Pyx_INCREF(__pyx_v_key);
     PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key);
     __Pyx_GIVEREF(__pyx_v_key);
@@ -7581,21 +7660,21 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
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     PyTuple_SET_ITEM(__pyx_t_2, 3, ((PyObject *)__pyx_n_s__Flag));
     __Pyx_GIVEREF(((PyObject *)__pyx_n_s__Flag));
-    __Pyx_INCREF(((PyObject *)__pyx_kp_s_63));
-    PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_63));
-    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_63));
-    __Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
-    PyTuple_SET_ITEM(__pyx_t_2, 5, ((PyObject *)__pyx_kp_s_9));
-    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
+    __Pyx_INCREF(((PyObject *)__pyx_kp_s_35));
+    PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_35));
+    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_35));
+    __Pyx_INCREF(((PyObject *)__pyx_kp_s_6));
+    PyTuple_SET_ITEM(__pyx_t_2, 5, ((PyObject *)__pyx_kp_s_6));
+    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6));
     __pyx_t_4 = 0;
-    __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyObject_Call(__pyx_t_3, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_4);
     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-    __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
     if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-    /* "cvcf.pyx":434
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":434
  *         if data == None:
  *             formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
  *             return             # <<<<<<<<<<<<<<
@@ -7609,7 +7688,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
   }
   __pyx_L7:;
 
-  /* "cvcf.pyx":435
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":435
  *             formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
  *             return
  *         if data == []: data = [""]             # unsure what type -- say string             # <<<<<<<<<<<<<<
@@ -7636,7 +7715,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
   }
   __pyx_L8:;
 
-  /* "cvcf.pyx":436
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":436
  *             return
  *         if data == []: data = [""]             # unsure what type -- say string
  *         if type(data[0]) == type(0.0):             # <<<<<<<<<<<<<<
@@ -7655,7 +7734,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
   if (__pyx_t_1) {
 
-    /* "cvcf.pyx":437
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":437
  *         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)             # <<<<<<<<<<<<<<
@@ -7667,7 +7746,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
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-    __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+    __Pyx_GOTREF(__pyx_t_2);
     __Pyx_INCREF(__pyx_v_key);
     PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key);
     __Pyx_GIVEREF(__pyx_v_key);
@@ -7679,21 +7758,21 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
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     PyTuple_SET_ITEM(__pyx_t_2, 3, ((PyObject *)__pyx_n_s__Float));
     __Pyx_GIVEREF(((PyObject *)__pyx_n_s__Float));
-    __Pyx_INCREF(((PyObject *)__pyx_kp_s_63));
-    PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_63));
-    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_63));
+    __Pyx_INCREF(((PyObject *)__pyx_kp_s_35));
+    PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_35));
+    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_35));
     __Pyx_INCREF(Py_None);
     PyTuple_SET_ITEM(__pyx_t_2, 5, Py_None);
     __Pyx_GIVEREF(Py_None);
     __pyx_t_4 = 0;
-    __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyObject_Call(__pyx_t_3, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-    __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
     if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-    /* "cvcf.pyx":438
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":438
  *         if type(data[0]) == type(0.0):
  *             formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
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@@ -7707,7 +7786,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
   }
   __pyx_L9:;
 
-  /* "cvcf.pyx":439
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":439
  *             formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
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  *         if type(data[0]) == type(0):             # <<<<<<<<<<<<<<
@@ -7723,7 +7802,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   if (__pyx_t_1) {
 
-    /* "cvcf.pyx":440
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":440
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  *             formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)             # <<<<<<<<<<<<<<
@@ -7735,7 +7814,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
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     __Pyx_GOTREF(__pyx_t_4);
     __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+    __Pyx_GOTREF(__pyx_t_3);
     __Pyx_INCREF(__pyx_v_key);
     PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_key);
     __Pyx_GIVEREF(__pyx_v_key);
@@ -7747,21 +7826,21 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
     __Pyx_INCREF(((PyObject *)__pyx_n_s__Integer));
     PyTuple_SET_ITEM(__pyx_t_3, 3, ((PyObject *)__pyx_n_s__Integer));
     __Pyx_GIVEREF(((PyObject *)__pyx_n_s__Integer));
-    __Pyx_INCREF(((PyObject *)__pyx_kp_s_63));
-    PyTuple_SET_ITEM(__pyx_t_3, 4, ((PyObject *)__pyx_kp_s_63));
-    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_63));
+    __Pyx_INCREF(((PyObject *)__pyx_kp_s_35));
+    PyTuple_SET_ITEM(__pyx_t_3, 4, ((PyObject *)__pyx_kp_s_35));
+    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_35));
     __Pyx_INCREF(Py_None);
     PyTuple_SET_ITEM(__pyx_t_3, 5, Py_None);
     __Pyx_GIVEREF(Py_None);
     __pyx_t_4 = 0;
-    __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyObject_Call(__pyx_t_2, __pyx_t_3, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_4);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-    __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
     if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-    /* "cvcf.pyx":441
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":441
  *         if type(data[0]) == type(0):
  *             formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
  *             return             # <<<<<<<<<<<<<<
@@ -7775,7 +7854,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
   }
   __pyx_L10:;
 
-  /* "cvcf.pyx":442
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":442
  *             formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
  *             return
  *         formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".")             # <<<<<<<<<<<<<<
@@ -7787,7 +7866,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+  __Pyx_GOTREF(__pyx_t_2);
   __Pyx_INCREF(__pyx_v_key);
   PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key);
   __Pyx_GIVEREF(__pyx_v_key);
@@ -7799,17 +7878,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
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   PyTuple_SET_ITEM(__pyx_t_2, 3, ((PyObject *)__pyx_n_s__String));
   __Pyx_GIVEREF(((PyObject *)__pyx_n_s__String));
-  __Pyx_INCREF(((PyObject *)__pyx_kp_s_63));
-  PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_63));
-  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_63));
-  __Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
-  PyTuple_SET_ITEM(__pyx_t_2, 5, ((PyObject *)__pyx_kp_s_9));
-  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
+  __Pyx_INCREF(((PyObject *)__pyx_kp_s_35));
+  PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_35));
+  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_35));
+  __Pyx_INCREF(((PyObject *)__pyx_kp_s_6));
+  PyTuple_SET_ITEM(__pyx_t_2, 5, ((PyObject *)__pyx_kp_s_6));
+  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6));
   __pyx_t_3 = 0;
-  __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(__pyx_t_4, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
@@ -7828,7 +7907,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
   return __pyx_r;
 }
 
-/* "cvcf.pyx":446
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":446
  * 
  *     # todo: trim trailing missing values
  *     def format_formatdata( self, data, format, key=True, value=True, separator=":" ):             # <<<<<<<<<<<<<<
@@ -7836,9 +7915,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb
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-static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_6format_formatdata = {__Pyx_NAMESTR("format_formatdata"), (PyCFunction)__pyx_pf_4cvcf_3VCF_6format_formatdata, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
-static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_format_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_format_formatdata = {__Pyx_NAMESTR("format_formatdata"), (PyCFunction)__pyx_pf_4cvcf_3VCF_format_formatdata, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pf_4cvcf_3VCF_format_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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   PyObject *__pyx_v_data = 0;
   PyObject *__pyx_v_format = 0;
@@ -7870,9 +7949,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
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     Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
     PyObject* values[6] = {0,0,0,0,0,0};
-    values[3] = __pyx_k_64;
-    values[4] = __pyx_k_65;
-    values[5] = ((PyObject *)__pyx_kp_s_4);
+    values[3] = __pyx_k_36;
+    values[4] = __pyx_k_37;
+    values[5] = ((PyObject *)__pyx_kp_s_3);
     switch (PyTuple_GET_SIZE(__pyx_args)) {
       case  6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
       case  5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
@@ -7926,9 +8005,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
     __pyx_v_value = values[4];
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   } else {
-    __pyx_v_key = __pyx_k_64;
-    __pyx_v_value = __pyx_k_65;
-    __pyx_v_separator = ((PyObject *)__pyx_kp_s_4);
+    __pyx_v_key = __pyx_k_36;
+    __pyx_v_value = __pyx_k_37;
+    __pyx_v_separator = ((PyObject *)__pyx_kp_s_3);
     switch (PyTuple_GET_SIZE(__pyx_args)) {
       case  6:
       __pyx_v_separator = PyTuple_GET_ITEM(__pyx_args, 5);
@@ -7953,15 +8032,15 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
   return NULL;
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-  __pyx_v_output = ((PyObject*)Py_None); __Pyx_INCREF(Py_None);
-  __pyx_v_sdata = ((PyObject*)Py_None); __Pyx_INCREF(Py_None);
-  __pyx_v_d = ((PyObject*)Py_None); __Pyx_INCREF(Py_None);
+  __pyx_v_output = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
+  __pyx_v_sdata = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
+  __pyx_v_d = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
   __pyx_v_k = Py_None; __Pyx_INCREF(Py_None);
   __pyx_v_idx = Py_None; __Pyx_INCREF(Py_None);
   __pyx_v_v = Py_None; __Pyx_INCREF(Py_None);
   __pyx_v_last = Py_None; __Pyx_INCREF(Py_None);
 
-  /* "cvcf.pyx":447
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":447
  *     # todo: trim trailing missing values
  *     def format_formatdata( self, data, format, key=True, value=True, separator=":" ):
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@@ -7979,7 +8058,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
   __pyx_v_sdata = __pyx_t_2;
   __pyx_t_2 = 0;
 
-  /* "cvcf.pyx":448
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":448
  *     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             # <<<<<<<<<<<<<<
@@ -7995,7 +8074,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   if (__pyx_t_3) {
 
-    /* "cvcf.pyx":449
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":449
  *         output, sdata = [], []
  *         if type(data) == type([]): # for FORMAT field, make data with dummy values
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@@ -8008,7 +8087,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
     __pyx_v_d = __pyx_t_1;
     __pyx_t_1 = 0;
 
-    /* "cvcf.pyx":450
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":450
  *         if type(data) == type([]): # for FORMAT field, make data with dummy values
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  *             for k in data: d[k] = []             # <<<<<<<<<<<<<<
@@ -8046,7 +8125,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
     }
     __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-    /* "cvcf.pyx":451
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":451
  *             d = {}
  *             for k in data: d[k] = []
  *             data = d             # <<<<<<<<<<<<<<
@@ -8060,7 +8139,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
   }
   __pyx_L6:;
 
-  /* "cvcf.pyx":453
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":453
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  *         for k in data:             # <<<<<<<<<<<<<<
@@ -8092,7 +8171,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
     __pyx_v_k = __pyx_t_2;
     __pyx_t_2 = 0;
 
-    /* "cvcf.pyx":454
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":454
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  *             self._add_definition( format, k, data[k], "(output)" )             # <<<<<<<<<<<<<<
@@ -8104,7 +8183,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
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-    __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+    __Pyx_GOTREF(__pyx_t_6);
     __Pyx_INCREF(__pyx_v_format);
     PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_format);
     __Pyx_GIVEREF(__pyx_v_format);
@@ -8113,17 +8192,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
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     PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_5);
     __Pyx_GIVEREF(__pyx_t_5);
-    __Pyx_INCREF(((PyObject *)__pyx_kp_s_66));
-    PyTuple_SET_ITEM(__pyx_t_6, 3, ((PyObject *)__pyx_kp_s_66));
-    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_66));
+    __Pyx_INCREF(((PyObject *)__pyx_kp_s_38));
+    PyTuple_SET_ITEM(__pyx_t_6, 3, ((PyObject *)__pyx_kp_s_38));
+    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_38));
     __pyx_t_5 = 0;
-    __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_5 = PyObject_Call(__pyx_t_2, __pyx_t_6, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_5);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-    __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
     __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
 
-    /* "cvcf.pyx":455
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":455
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  *             for idx,v in enumerate(data[k]):             # <<<<<<<<<<<<<<
@@ -8168,7 +8247,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
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-      /* "cvcf.pyx":456
+      /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":456
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@@ -8188,7 +8267,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
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@@ -8199,7 +8278,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
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-  /* "cvcf.pyx":458
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":458
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-    /* "cvcf.pyx":459
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":459
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@@ -8249,22 +8328,22 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
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-      __Pyx_GOTREF(((PyObject *)__pyx_t_2));
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-      __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
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-  /* "cvcf.pyx":460
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":460
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@@ -8276,7 +8355,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
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-  /* "cvcf.pyx":461
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":461
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-    /* "cvcf.pyx":462
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":462
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@@ -8298,18 +8377,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
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-    __Pyx_GOTREF(((PyObject *)__pyx_t_5));
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+    __pyx_t_2 = PyObject_Call(__pyx_builtin_map, __pyx_t_5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
     __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+    __Pyx_GOTREF(__pyx_t_5);
     __Pyx_INCREF(((PyObject *)__pyx_n_s__GT));
     PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_n_s__GT));
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@@ -8318,8 +8397,8 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
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-    PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_5));
-    __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
+    PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
+    __Pyx_GIVEREF(__pyx_t_5);
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@@ -8331,17 +8410,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
   }
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-  /* "cvcf.pyx":463
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":463
  *         if 'GT' in data:
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  *         for k,v in sdata:             # <<<<<<<<<<<<<<
  *             if v == []: v = None
  *             if key and value:
  */
-  if (unlikely(__pyx_v_sdata == Py_None)) {
-    PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 
+  if (likely(((PyObject *)__pyx_v_sdata) != Py_None)) {
+    __pyx_t_4 = 0; __pyx_t_5 = ((PyObject *)__pyx_v_sdata); __Pyx_INCREF(__pyx_t_5);
+  } else {
+    PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -8374,7 +8454,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
       __pyx_t_6 = 0;
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-    /* "cvcf.pyx":464
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":464
  *             sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
  *         for k,v in sdata:
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@@ -8396,7 +8476,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
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-    /* "cvcf.pyx":465
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":465
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@@ -8412,7 +8492,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
     }
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-      /* "cvcf.pyx":466
+      /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":466
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@@ -8427,41 +8507,41 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py
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-        __Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
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+        __Pyx_INCREF(((PyObject *)((PyObject*)&PyString_Type)));
+        PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)((PyObject*)&PyString_Type)));
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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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+        __pyx_t_9 = PyList_Append(((PyObject *)__pyx_v_output), __pyx_t_1); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "cvcf.pyx":467
+        /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":467
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+        __pyx_t_9 = PyList_Append(((PyObject *)__pyx_v_output), __pyx_v_k); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "cvcf.pyx":468
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":468
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+      __pyx_t_9 = PyList_Append(((PyObject *)__pyx_v_output), __pyx_v_k); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       goto __pyx_L21;
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-    /* "cvcf.pyx":469
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":469
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  *             elif value:             # <<<<<<<<<<<<<<
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     if (__pyx_t_11) {
 
-      /* "cvcf.pyx":470
+      /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":470
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-static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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+static PyMethodDef __pyx_mdef_4cvcf_3VCF_convertGT = {__Pyx_NAMESTR("convertGT"), (PyCFunction)__pyx_pf_4cvcf_3VCF_convertGT, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pf_4cvcf_3VCF_convertGT(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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-    PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_9));
-    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
+    __Pyx_INCREF(((PyObject *)__pyx_kp_s_6));
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+    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6));
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-        __Pyx_GOTREF(((PyObject *)__pyx_t_1));
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+        __pyx_t_1 = PyObject_RichCompare(__pyx_t_4, ((PyObject *)__pyx_kp_s_6), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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@@ -10730,7 +10866,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject
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-      __Pyx_GOTREF(((PyObject *)__pyx_t_3));
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-      __Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
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-      __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
-      __Pyx_INCREF(((PyObject *)__pyx_kp_s_92));
-      PyList_SET_ITEM(__pyx_t_12, 1, ((PyObject *)__pyx_kp_s_92));
-      __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_92));
-      __Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
-      PyList_SET_ITEM(__pyx_t_12, 2, ((PyObject *)__pyx_kp_s_9));
-      __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
+      __Pyx_INCREF(((PyObject *)__pyx_kp_s_6));
+      PyList_SET_ITEM(__pyx_t_12, 0, ((PyObject *)__pyx_kp_s_6));
+      __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6));
+      __Pyx_INCREF(((PyObject *)__pyx_kp_s_57));
+      PyList_SET_ITEM(__pyx_t_12, 1, ((PyObject *)__pyx_kp_s_57));
+      __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_57));
+      __Pyx_INCREF(((PyObject *)__pyx_kp_s_6));
+      PyList_SET_ITEM(__pyx_t_12, 2, ((PyObject *)__pyx_kp_s_6));
+      __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6));
       __pyx_r = ((PyObject *)__pyx_t_12);
       __pyx_t_12 = 0;
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@@ -10935,7 +11071,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject
   return __pyx_r;
 }
 
-/* "cvcf.pyx":569
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":569
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@@ -10943,9 +11079,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject
  * 
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_13convertGTback(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_13convertGTback = {__Pyx_NAMESTR("convertGTback"), (PyCFunction)__pyx_pf_4cvcf_3VCF_13convertGTback, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
-static PyObject *__pyx_pf_4cvcf_3VCF_13convertGTback(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_convertGTback(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_convertGTback = {__Pyx_NAMESTR("convertGTback"), (PyCFunction)__pyx_pf_4cvcf_3VCF_convertGTback, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pf_4cvcf_3VCF_convertGTback(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_GTdata = 0;
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@@ -10996,7 +11132,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_13convertGTback(PyObject *__pyx_self, PyObj
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":570
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":570
  * 
  *     def convertGTback(self, GTdata):
  *         return ''.join(map(str,GTdata))             # <<<<<<<<<<<<<<
@@ -11007,25 +11143,25 @@ static PyObject *__pyx_pf_4cvcf_3VCF_13convertGTback(PyObject *__pyx_self, PyObj
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
-  __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
-  PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
-  __Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
+  __Pyx_GOTREF(__pyx_t_2);
+  __Pyx_INCREF(((PyObject *)((PyObject*)&PyString_Type)));
+  PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)((PyObject*)&PyString_Type)));
+  __Pyx_GIVEREF(((PyObject *)((PyObject*)&PyString_Type)));
   __Pyx_INCREF(__pyx_v_GTdata);
   PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_GTdata);
   __Pyx_GIVEREF(__pyx_v_GTdata);
-  __pyx_t_3 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(__pyx_builtin_map, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+  __Pyx_GOTREF(__pyx_t_2);
   PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3);
   __Pyx_GIVEREF(__pyx_t_3);
   __pyx_t_3 = 0;
-  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __pyx_r = __pyx_t_3;
   __pyx_t_3 = 0;
   goto __pyx_L0;
@@ -11044,7 +11180,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_13convertGTback(PyObject *__pyx_self, PyObj
   return __pyx_r;
 }
 
-/* "cvcf.pyx":572
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":572
  *         return ''.join(map(str,GTdata))
  * 
  *     def parse_formatdata( self, key, value, formatdict, line ):             # <<<<<<<<<<<<<<
@@ -11052,9 +11188,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_13convertGTback(PyObject *__pyx_self, PyObj
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  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_14parse_formatdata = {__Pyx_NAMESTR("parse_formatdata"), (PyCFunction)__pyx_pf_4cvcf_3VCF_14parse_formatdata, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
-static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_parse_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_parse_formatdata = {__Pyx_NAMESTR("parse_formatdata"), (PyCFunction)__pyx_pf_4cvcf_3VCF_parse_formatdata, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pf_4cvcf_3VCF_parse_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_key = 0;
   PyObject *__pyx_v_value = 0;
@@ -11154,7 +11290,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, Py
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   __pyx_v_v = Py_None; __Pyx_INCREF(Py_None);
 
-  /* "cvcf.pyx":574
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":574
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@@ -11164,22 +11300,22 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, Py
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+  __Pyx_GOTREF(__pyx_t_2);
   __Pyx_INCREF(__pyx_v_key);
   PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key);
   __Pyx_GIVEREF(__pyx_v_key);
   __Pyx_INCREF(Py_None);
   PyTuple_SET_ITEM(__pyx_t_2, 1, Py_None);
   __Pyx_GIVEREF(Py_None);
-  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_v_f);
   __pyx_v_f = __pyx_t_3;
   __pyx_t_3 = 0;
 
-  /* "cvcf.pyx":575
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":575
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  *         f = formatdict.get(key,None)
  *         if f == None:             # <<<<<<<<<<<<<<
@@ -11192,7 +11328,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, Py
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
   if (__pyx_t_4) {
 
-    /* "cvcf.pyx":576
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":576
  *         f = formatdict.get(key,None)
  *         if f == None:
  *             self._add_definition(formatdict, key, value, line )             # <<<<<<<<<<<<<<
@@ -11202,7 +11338,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, Py
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     __Pyx_GOTREF(__pyx_t_3);
     __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+    __Pyx_GOTREF(__pyx_t_2);
     __Pyx_INCREF(__pyx_v_formatdict);
     PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_formatdict);
     __Pyx_GIVEREF(__pyx_v_formatdict);
@@ -11215,13 +11351,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, Py
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     PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_v_line);
     __Pyx_GIVEREF(__pyx_v_line);
-    __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_1 = PyObject_Call(__pyx_t_3, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-    __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
     __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-    /* "cvcf.pyx":577
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":577
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@@ -11237,7 +11373,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, Py
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-  /* "cvcf.pyx":578
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":578
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@@ -11253,7 +11389,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, Py
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-    /* "cvcf.pyx":579
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":579
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@@ -11264,26 +11400,26 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, Py
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+      __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_58); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+      __Pyx_GOTREF(__pyx_t_3);
       __Pyx_INCREF(__pyx_v_line);
       PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_line);
       __Pyx_GIVEREF(__pyx_v_line);
       PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1);
       __Pyx_GIVEREF(__pyx_t_1);
       __pyx_t_1 = 0;
-      __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_1 = PyObject_Call(__pyx_t_2, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_1);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-      __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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-    /* "cvcf.pyx":580
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":580
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@@ -11300,7 +11436,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, Py
   }
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-  /* "cvcf.pyx":581
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@@ -11309,56 +11445,68 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, Py
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   __Pyx_GOTREF(__pyx_t_1);
-  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_94), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
+  __Pyx_INCREF(((PyObject *)__pyx_kp_s_2));
+  PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_kp_s_2));
+  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
+  __pyx_t_2 = PyObject_Call(__pyx_t_1, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_2);
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
   __Pyx_DECREF(__pyx_v_values);
-  __pyx_v_values = __pyx_t_3;
-  __pyx_t_3 = 0;
+  __pyx_v_values = __pyx_t_2;
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-  /* "cvcf.pyx":583
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-        __Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
-        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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-        __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
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-        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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@@ -12054,29 +12208,29 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, Py
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-    /* "cvcf.pyx":612
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-      /* "cvcf.pyx":779
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+      __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_6 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __Pyx_GOTREF(__pyx_t_6);
+      __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
       __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
       goto __pyx_L8;
     }
     /*else*/ {
 
-      /* "cvcf.pyx":861
+      /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":861
  *                 self.enter_default_format()
  *             else:
  *                 break             # <<<<<<<<<<<<<<
@@ -17380,7 +17601,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18_parse_header(PyObject *__pyx_self, PyObj
   __pyx_L7_break:;
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-  /* "cvcf.pyx":862
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":862
  *             else:
  *                 break
  *         return line             # <<<<<<<<<<<<<<
@@ -17398,7 +17619,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18_parse_header(PyObject *__pyx_self, PyObj
   __Pyx_XDECREF(__pyx_t_2);
   __Pyx_XDECREF(__pyx_t_3);
   __Pyx_XDECREF(__pyx_t_4);
-  __Pyx_XDECREF(__pyx_t_6);
+  __Pyx_XDECREF(__pyx_t_5);
   __Pyx_AddTraceback("cvcf.VCF._parse_header");
   __pyx_r = NULL;
   __pyx_L0:;
@@ -17408,7 +17629,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18_parse_header(PyObject *__pyx_self, PyObj
   return __pyx_r;
 }
 
-/* "cvcf.pyx":864
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":864
  *         return line
  * 
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@@ -17416,9 +17637,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18_parse_header(PyObject *__pyx_self, PyObj
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  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_19_parse = {__Pyx_NAMESTR("_parse"), (PyCFunction)__pyx_pf_4cvcf_3VCF_19_parse, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
-static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF__parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_4cvcf_3VCF__parse = {__Pyx_NAMESTR("_parse"), (PyCFunction)__pyx_pf_4cvcf_3VCF__parse, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pf_4cvcf_3VCF__parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_line = 0;
   PyObject *__pyx_v_stream = 0;
@@ -17487,7 +17708,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__
   __Pyx_INCREF(__pyx_v_line);
   __pyx_v_d = Py_None; __Pyx_INCREF(Py_None);
 
-  /* "cvcf.pyx":865
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":865
  * 
  *     def _parse(self, line, stream):
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@@ -17504,7 +17725,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__
   __pyx_t_4 = (__pyx_t_3 > 0);
   if (__pyx_t_4) {
 
-    /* "cvcf.pyx":866
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":866
  *     def _parse(self, line, stream):
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@@ -17519,14 +17740,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__
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-    __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+    __Pyx_GOTREF(__pyx_t_1);
     PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_5);
     __Pyx_GIVEREF(__pyx_t_5);
     __pyx_t_5 = 0;
-    __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_5 = PyObject_Call(__pyx_t_2, __pyx_t_1, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_5);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-    __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
     __Pyx_DECREF(__pyx_v_d);
     __pyx_v_d = __pyx_t_5;
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@@ -17534,7 +17755,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__
   }
   __pyx_L6:;
 
-  /* "cvcf.pyx":868
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":868
  *             d = self.parse_data( line.strip() )
  *             #if d: yield d
  *         for line in stream:             # <<<<<<<<<<<<<<
@@ -17566,7 +17787,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__
     __pyx_v_line = __pyx_t_1;
     __pyx_t_1 = 0;
 
-    /* "cvcf.pyx":869
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":869
  *             #if d: yield d
  *         for line in stream:
  *             self._lineno += 1             # <<<<<<<<<<<<<<
@@ -17581,7 +17802,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__
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     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-    /* "cvcf.pyx":870
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":870
  *         for line in stream:
  *             self._lineno += 1
  *             if self._lines and self._lineno > self._lines: raise StopIteration             # <<<<<<<<<<<<<<
@@ -17614,7 +17835,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__
     }
     __pyx_L9:;
 
-    /* "cvcf.pyx":871
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":871
  *             self._lineno += 1
  *             if self._lines and self._lineno > self._lines: raise StopIteration
  *             d = self.parse_data( line.strip() )             # <<<<<<<<<<<<<<
@@ -17629,14 +17850,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__
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-    __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+    __Pyx_GOTREF(__pyx_t_1);
     PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
     __Pyx_GIVEREF(__pyx_t_2);
     __pyx_t_2 = 0;
-    __pyx_t_2 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyObject_Call(__pyx_t_6, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
-    __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
     __Pyx_DECREF(__pyx_v_d);
     __pyx_v_d = __pyx_t_2;
     __pyx_t_2 = 0;
@@ -17660,7 +17881,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__
   return __pyx_r;
 }
 
-/* "cvcf.pyx":880
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":880
  *     ######################################################################################################
  * 
  *     def getsamples(self):             # <<<<<<<<<<<<<<
@@ -17668,16 +17889,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__
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-static PyObject *__pyx_pf_4cvcf_3VCF_20getsamples(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_20getsamples[] = " List of samples in VCF file ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_20getsamples = {__Pyx_NAMESTR("getsamples"), (PyCFunction)__pyx_pf_4cvcf_3VCF_20getsamples, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_20getsamples)};
-static PyObject *__pyx_pf_4cvcf_3VCF_20getsamples(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_4cvcf_3VCF_getsamples(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_getsamples[] = " List of samples in VCF file ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_getsamples = {__Pyx_NAMESTR("getsamples"), (PyCFunction)__pyx_pf_4cvcf_3VCF_getsamples, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_getsamples)};
+static PyObject *__pyx_pf_4cvcf_3VCF_getsamples(PyObject *__pyx_self, PyObject *__pyx_v_self) {
   PyObject *__pyx_r = NULL;
   PyObject *__pyx_t_1 = NULL;
   __Pyx_RefNannySetupContext("getsamples");
   __pyx_self = __pyx_self;
 
-  /* "cvcf.pyx":882
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":882
  *     def getsamples(self):
  *         """ List of samples in VCF file """
  *         return self._samples             # <<<<<<<<<<<<<<
@@ -17703,7 +17924,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20getsamples(PyObject *__pyx_self, PyObject
   return __pyx_r;
 }
 
-/* "cvcf.pyx":884
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":884
  *         return self._samples
  * 
  *     def setsamples(self,samples):             # <<<<<<<<<<<<<<
@@ -17711,10 +17932,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20getsamples(PyObject *__pyx_self, PyObject
  *         self._samples = samples
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_21setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_21setsamples[] = " List of samples in VCF file ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_21setsamples = {__Pyx_NAMESTR("setsamples"), (PyCFunction)__pyx_pf_4cvcf_3VCF_21setsamples, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_21setsamples)};
-static PyObject *__pyx_pf_4cvcf_3VCF_21setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_setsamples[] = " List of samples in VCF file ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_setsamples = {__Pyx_NAMESTR("setsamples"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setsamples, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_setsamples)};
+static PyObject *__pyx_pf_4cvcf_3VCF_setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_samples = 0;
   PyObject *__pyx_r = NULL;
@@ -17762,7 +17983,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_21setsamples(PyObject *__pyx_self, PyObject
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":886
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":886
  *     def setsamples(self,samples):
  *         """ List of samples in VCF file """
  *         self._samples = samples             # <<<<<<<<<<<<<<
@@ -17782,7 +18003,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_21setsamples(PyObject *__pyx_self, PyObject
   return __pyx_r;
 }
 
-/* "cvcf.pyx":888
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":888
  *         self._samples = samples
  * 
  *     def getheader(self):             # <<<<<<<<<<<<<<
@@ -17790,16 +18011,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_21setsamples(PyObject *__pyx_self, PyObject
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-static PyObject *__pyx_pf_4cvcf_3VCF_22getheader(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_22getheader[] = " List of header key-value pairs (strings) ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_22getheader = {__Pyx_NAMESTR("getheader"), (PyCFunction)__pyx_pf_4cvcf_3VCF_22getheader, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_22getheader)};
-static PyObject *__pyx_pf_4cvcf_3VCF_22getheader(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_4cvcf_3VCF_getheader(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_getheader[] = " List of header key-value pairs (strings) ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_getheader = {__Pyx_NAMESTR("getheader"), (PyCFunction)__pyx_pf_4cvcf_3VCF_getheader, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_getheader)};
+static PyObject *__pyx_pf_4cvcf_3VCF_getheader(PyObject *__pyx_self, PyObject *__pyx_v_self) {
   PyObject *__pyx_r = NULL;
   PyObject *__pyx_t_1 = NULL;
   __Pyx_RefNannySetupContext("getheader");
   __pyx_self = __pyx_self;
 
-  /* "cvcf.pyx":890
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":890
  *     def getheader(self):
  *         """ List of header key-value pairs (strings) """
  *         return self._header             # <<<<<<<<<<<<<<
@@ -17825,7 +18046,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_22getheader(PyObject *__pyx_self, PyObject
   return __pyx_r;
 }
 
-/* "cvcf.pyx":892
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":892
  *         return self._header
  * 
  *     def setheader(self,header):             # <<<<<<<<<<<<<<
@@ -17833,10 +18054,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_22getheader(PyObject *__pyx_self, PyObject
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-static PyObject *__pyx_pf_4cvcf_3VCF_23setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_23setheader[] = " List of header key-value pairs (strings) ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_23setheader = {__Pyx_NAMESTR("setheader"), (PyCFunction)__pyx_pf_4cvcf_3VCF_23setheader, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_23setheader)};
-static PyObject *__pyx_pf_4cvcf_3VCF_23setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_setheader[] = " List of header key-value pairs (strings) ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_setheader = {__Pyx_NAMESTR("setheader"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setheader, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_setheader)};
+static PyObject *__pyx_pf_4cvcf_3VCF_setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_header = 0;
   PyObject *__pyx_r = NULL;
@@ -17884,7 +18105,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_23setheader(PyObject *__pyx_self, PyObject
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":894
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":894
  *     def setheader(self,header):
  *         """ List of header key-value pairs (strings) """
  *         self._header = header             # <<<<<<<<<<<<<<
@@ -17904,7 +18125,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_23setheader(PyObject *__pyx_self, PyObject
   return __pyx_r;
 }
 
-/* "cvcf.pyx":896
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":896
  *         self._header = header
  * 
  *     def getinfo(self):             # <<<<<<<<<<<<<<
@@ -17912,16 +18133,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_23setheader(PyObject *__pyx_self, PyObject
  *         return self._info
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-static PyObject *__pyx_pf_4cvcf_3VCF_24getinfo(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_24getinfo[] = " Dictionary of ##INFO tags, as VCF.FORMAT values ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_24getinfo = {__Pyx_NAMESTR("getinfo"), (PyCFunction)__pyx_pf_4cvcf_3VCF_24getinfo, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_24getinfo)};
-static PyObject *__pyx_pf_4cvcf_3VCF_24getinfo(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_4cvcf_3VCF_getinfo(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_getinfo[] = " Dictionary of ##INFO tags, as VCF.FORMAT values ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_getinfo = {__Pyx_NAMESTR("getinfo"), (PyCFunction)__pyx_pf_4cvcf_3VCF_getinfo, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_getinfo)};
+static PyObject *__pyx_pf_4cvcf_3VCF_getinfo(PyObject *__pyx_self, PyObject *__pyx_v_self) {
   PyObject *__pyx_r = NULL;
   PyObject *__pyx_t_1 = NULL;
   __Pyx_RefNannySetupContext("getinfo");
   __pyx_self = __pyx_self;
 
-  /* "cvcf.pyx":898
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":898
  *     def getinfo(self):
  *         """ Dictionary of ##INFO tags, as VCF.FORMAT values """
  *         return self._info             # <<<<<<<<<<<<<<
@@ -17947,7 +18168,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24getinfo(PyObject *__pyx_self, PyObject *_
   return __pyx_r;
 }
 
-/* "cvcf.pyx":900
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":900
  *         return self._info
  * 
  *     def setinfo(self,info):             # <<<<<<<<<<<<<<
@@ -17955,10 +18176,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24getinfo(PyObject *__pyx_self, PyObject *_
  *         self._info = info
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_25setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_25setinfo[] = " Dictionary of ##INFO tags, as VCF.FORMAT values ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_25setinfo = {__Pyx_NAMESTR("setinfo"), (PyCFunction)__pyx_pf_4cvcf_3VCF_25setinfo, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_25setinfo)};
-static PyObject *__pyx_pf_4cvcf_3VCF_25setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_setinfo[] = " Dictionary of ##INFO tags, as VCF.FORMAT values ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_setinfo = {__Pyx_NAMESTR("setinfo"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setinfo, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_setinfo)};
+static PyObject *__pyx_pf_4cvcf_3VCF_setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_info = 0;
   PyObject *__pyx_r = NULL;
@@ -18006,7 +18227,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_25setinfo(PyObject *__pyx_self, PyObject *_
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":902
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":902
  *     def setinfo(self,info):
  *         """ Dictionary of ##INFO tags, as VCF.FORMAT values """
  *         self._info = info             # <<<<<<<<<<<<<<
@@ -18026,7 +18247,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_25setinfo(PyObject *__pyx_self, PyObject *_
   return __pyx_r;
 }
 
-/* "cvcf.pyx":904
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":904
  *         self._info = info
  * 
  *     def getformat(self):             # <<<<<<<<<<<<<<
@@ -18034,16 +18255,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_25setinfo(PyObject *__pyx_self, PyObject *_
  *         return self._format
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_26getformat(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_26getformat[] = " Dictionary of ##FORMAT tags, as VCF.FORMAT values ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_26getformat = {__Pyx_NAMESTR("getformat"), (PyCFunction)__pyx_pf_4cvcf_3VCF_26getformat, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_26getformat)};
-static PyObject *__pyx_pf_4cvcf_3VCF_26getformat(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_4cvcf_3VCF_getformat(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_getformat[] = " Dictionary of ##FORMAT tags, as VCF.FORMAT values ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_getformat = {__Pyx_NAMESTR("getformat"), (PyCFunction)__pyx_pf_4cvcf_3VCF_getformat, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_getformat)};
+static PyObject *__pyx_pf_4cvcf_3VCF_getformat(PyObject *__pyx_self, PyObject *__pyx_v_self) {
   PyObject *__pyx_r = NULL;
   PyObject *__pyx_t_1 = NULL;
   __Pyx_RefNannySetupContext("getformat");
   __pyx_self = __pyx_self;
 
-  /* "cvcf.pyx":906
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":906
  *     def getformat(self):
  *         """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
  *         return self._format             # <<<<<<<<<<<<<<
@@ -18069,7 +18290,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_26getformat(PyObject *__pyx_self, PyObject
   return __pyx_r;
 }
 
-/* "cvcf.pyx":908
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":908
  *         return self._format
  * 
  *     def setformat(self,format):             # <<<<<<<<<<<<<<
@@ -18077,10 +18298,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_26getformat(PyObject *__pyx_self, PyObject
  *         self._format = format
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_27setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_27setformat[] = " Dictionary of ##FORMAT tags, as VCF.FORMAT values ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_27setformat = {__Pyx_NAMESTR("setformat"), (PyCFunction)__pyx_pf_4cvcf_3VCF_27setformat, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_27setformat)};
-static PyObject *__pyx_pf_4cvcf_3VCF_27setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_setformat[] = " Dictionary of ##FORMAT tags, as VCF.FORMAT values ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_setformat = {__Pyx_NAMESTR("setformat"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setformat, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_setformat)};
+static PyObject *__pyx_pf_4cvcf_3VCF_setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_format = 0;
   PyObject *__pyx_r = NULL;
@@ -18128,7 +18349,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_27setformat(PyObject *__pyx_self, PyObject
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":910
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":910
  *     def setformat(self,format):
  *         """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
  *         self._format = format             # <<<<<<<<<<<<<<
@@ -18148,7 +18369,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_27setformat(PyObject *__pyx_self, PyObject
   return __pyx_r;
 }
 
-/* "cvcf.pyx":912
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":912
  *         self._format = format
  * 
  *     def getfilter(self):             # <<<<<<<<<<<<<<
@@ -18156,16 +18377,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_27setformat(PyObject *__pyx_self, PyObject
  *         return self._filter
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_28getfilter(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_28getfilter[] = " Dictionary of ##FILTER tags, as VCF.FORMAT values ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_28getfilter = {__Pyx_NAMESTR("getfilter"), (PyCFunction)__pyx_pf_4cvcf_3VCF_28getfilter, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_28getfilter)};
-static PyObject *__pyx_pf_4cvcf_3VCF_28getfilter(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_4cvcf_3VCF_getfilter(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_getfilter[] = " Dictionary of ##FILTER tags, as VCF.FORMAT values ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_getfilter = {__Pyx_NAMESTR("getfilter"), (PyCFunction)__pyx_pf_4cvcf_3VCF_getfilter, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_getfilter)};
+static PyObject *__pyx_pf_4cvcf_3VCF_getfilter(PyObject *__pyx_self, PyObject *__pyx_v_self) {
   PyObject *__pyx_r = NULL;
   PyObject *__pyx_t_1 = NULL;
   __Pyx_RefNannySetupContext("getfilter");
   __pyx_self = __pyx_self;
 
-  /* "cvcf.pyx":914
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":914
  *     def getfilter(self):
  *         """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
  *         return self._filter             # <<<<<<<<<<<<<<
@@ -18191,7 +18412,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28getfilter(PyObject *__pyx_self, PyObject
   return __pyx_r;
 }
 
-/* "cvcf.pyx":916
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":916
  *         return self._filter
  * 
  *     def setfilter(self,filter):             # <<<<<<<<<<<<<<
@@ -18199,10 +18420,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28getfilter(PyObject *__pyx_self, PyObject
  *         self._filter = filter
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_29setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_29setfilter[] = " Dictionary of ##FILTER tags, as VCF.FORMAT values ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_29setfilter = {__Pyx_NAMESTR("setfilter"), (PyCFunction)__pyx_pf_4cvcf_3VCF_29setfilter, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_29setfilter)};
-static PyObject *__pyx_pf_4cvcf_3VCF_29setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_setfilter[] = " Dictionary of ##FILTER tags, as VCF.FORMAT values ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_setfilter = {__Pyx_NAMESTR("setfilter"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setfilter, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_setfilter)};
+static PyObject *__pyx_pf_4cvcf_3VCF_setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_filter = 0;
   PyObject *__pyx_r = NULL;
@@ -18250,7 +18471,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_29setfilter(PyObject *__pyx_self, PyObject
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":918
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":918
  *     def setfilter(self,filter):
  *         """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
  *         self._filter = filter             # <<<<<<<<<<<<<<
@@ -18270,7 +18491,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_29setfilter(PyObject *__pyx_self, PyObject
   return __pyx_r;
 }
 
-/* "cvcf.pyx":920
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":920
  *         self._filter = filter
  * 
  *     def setversion(self, version):             # <<<<<<<<<<<<<<
@@ -18278,9 +18499,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_29setfilter(PyObject *__pyx_self, PyObject
  *         self._version = version
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_30setversion = {__Pyx_NAMESTR("setversion"), (PyCFunction)__pyx_pf_4cvcf_3VCF_30setversion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
-static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_setversion = {__Pyx_NAMESTR("setversion"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setversion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pf_4cvcf_3VCF_setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_version = 0;
   PyObject *__pyx_r = NULL;
@@ -18288,6 +18509,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject
   int __pyx_t_2;
   int __pyx_t_3;
   int __pyx_t_4;
+  PyObject *__pyx_t_5 = NULL;
   static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__version,0};
   __Pyx_RefNannySetupContext("setversion");
   __pyx_self = __pyx_self;
@@ -18332,7 +18554,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":921
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":921
  * 
  *     def setversion(self, version):
  *         if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files")             # <<<<<<<<<<<<<<
@@ -18353,16 +18575,22 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject
     __pyx_t_4 = __pyx_t_2;
   }
   if (__pyx_t_4) {
-    __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_120), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_1);
-    __Pyx_Raise(__pyx_t_1, 0, 0);
+    __Pyx_INCREF(((PyObject *)__pyx_kp_s_70));
+    PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_70));
+    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_70));
+    __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_5);
     __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+    __Pyx_Raise(__pyx_t_5, 0, 0);
+    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
     {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     goto __pyx_L6;
   }
   __pyx_L6:;
 
-  /* "cvcf.pyx":922
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":922
  *     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             # <<<<<<<<<<<<<<
@@ -18375,6 +18603,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject
   goto __pyx_L0;
   __pyx_L1_error:;
   __Pyx_XDECREF(__pyx_t_1);
+  __Pyx_XDECREF(__pyx_t_5);
   __Pyx_AddTraceback("cvcf.VCF.setversion");
   __pyx_r = NULL;
   __pyx_L0:;
@@ -18383,7 +18612,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject
   return __pyx_r;
 }
 
-/* "cvcf.pyx":924
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":924
  *         self._version = version
  * 
  *     def setregions(self, regions):             # <<<<<<<<<<<<<<
@@ -18391,9 +18620,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject
  * 
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_31setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_31setregions = {__Pyx_NAMESTR("setregions"), (PyCFunction)__pyx_pf_4cvcf_3VCF_31setregions, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
-static PyObject *__pyx_pf_4cvcf_3VCF_31setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_setregions = {__Pyx_NAMESTR("setregions"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setregions, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pf_4cvcf_3VCF_setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_regions = 0;
   PyObject *__pyx_r = NULL;
@@ -18441,7 +18670,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_31setregions(PyObject *__pyx_self, PyObject
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":925
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":925
  * 
  *     def setregions(self, regions):
  *         self._regions = regions             # <<<<<<<<<<<<<<
@@ -18461,7 +18690,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_31setregions(PyObject *__pyx_self, PyObject
   return __pyx_r;
 }
 
-/* "cvcf.pyx":927
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":927
  *         self._regions = regions
  * 
  *     def setreference(self, ref):             # <<<<<<<<<<<<<<
@@ -18469,10 +18698,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_31setregions(PyObject *__pyx_self, PyObject
  *         self._reference = ref
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_32setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_32setreference[] = " Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_32setreference = {__Pyx_NAMESTR("setreference"), (PyCFunction)__pyx_pf_4cvcf_3VCF_32setreference, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_32setreference)};
-static PyObject *__pyx_pf_4cvcf_3VCF_32setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_setreference[] = " Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_setreference = {__Pyx_NAMESTR("setreference"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setreference, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_setreference)};
+static PyObject *__pyx_pf_4cvcf_3VCF_setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_ref = 0;
   PyObject *__pyx_r = NULL;
@@ -18520,7 +18749,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32setreference(PyObject *__pyx_self, PyObje
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":929
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":929
  *     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             # <<<<<<<<<<<<<<
@@ -18540,7 +18769,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32setreference(PyObject *__pyx_self, PyObje
   return __pyx_r;
 }
 
-/* "cvcf.pyx":931
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":931
  *         self._reference = ref
  * 
  *     def ignoreerror(self, errorstring):             # <<<<<<<<<<<<<<
@@ -18548,9 +18777,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32setreference(PyObject *__pyx_self, PyObje
  *         except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_33ignoreerror = {__Pyx_NAMESTR("ignoreerror"), (PyCFunction)__pyx_pf_4cvcf_3VCF_33ignoreerror, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
-static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_ignoreerror = {__Pyx_NAMESTR("ignoreerror"), (PyCFunction)__pyx_pf_4cvcf_3VCF_ignoreerror, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pf_4cvcf_3VCF_ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_errorstring = 0;
   PyObject *__pyx_r = NULL;
@@ -18604,7 +18833,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObjec
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":932
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":932
  * 
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@@ -18629,14 +18858,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObjec
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-      __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+      __Pyx_GOTREF(__pyx_t_1);
       PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3);
       __Pyx_GIVEREF(__pyx_t_3);
       __pyx_t_3 = 0;
-      __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L6_error;}
+      __pyx_t_3 = PyObject_Call(__pyx_t_2, __pyx_t_1, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L6_error;}
       __Pyx_GOTREF(__pyx_t_3);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-      __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
       __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
     }
     __Pyx_XDECREF(__pyx_save_exc_type); __pyx_save_exc_type = 0;
@@ -18648,7 +18877,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObjec
     __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
     __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-    /* "cvcf.pyx":933
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":933
  *     def ignoreerror(self, errorstring):
  *         try:             self._ignored_errors.add(self.__dict__[errorstring])
  *         except KeyError: raise ValueError("Invalid error string: %s" % errorstring)             # <<<<<<<<<<<<<<
@@ -18662,16 +18891,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObjec
       __Pyx_GOTREF(__pyx_t_3);
       __Pyx_GOTREF(__pyx_t_1);
       __Pyx_GOTREF(__pyx_t_2);
-      __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_121), __pyx_v_errorstring); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;}
+      __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_71), __pyx_v_errorstring); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;}
       __Pyx_GOTREF(((PyObject *)__pyx_t_5));
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-      __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+      __Pyx_GOTREF(__pyx_t_6);
       PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_5));
       __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
       __pyx_t_5 = 0;
-      __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;}
+      __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;}
       __Pyx_GOTREF(__pyx_t_5);
-      __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
       __Pyx_Raise(__pyx_t_5, 0, 0);
       __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
       {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;}
@@ -18710,7 +18939,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObjec
   return __pyx_r;
 }
 
-/* "cvcf.pyx":935
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":935
  *         except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
  * 
  *     def warnerror(self, errorstring):             # <<<<<<<<<<<<<<
@@ -18718,9 +18947,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObjec
  *         except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_34warnerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_34warnerror = {__Pyx_NAMESTR("warnerror"), (PyCFunction)__pyx_pf_4cvcf_3VCF_34warnerror, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
-static PyObject *__pyx_pf_4cvcf_3VCF_34warnerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_warnerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_warnerror = {__Pyx_NAMESTR("warnerror"), (PyCFunction)__pyx_pf_4cvcf_3VCF_warnerror, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pf_4cvcf_3VCF_warnerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_errorstring = 0;
   PyObject *__pyx_r = NULL;
@@ -18774,7 +19003,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34warnerror(PyObject *__pyx_self, PyObject
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":936
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":936
  * 
  *     def warnerror(self, errorstring):
  *         try:             self._warn_errors.add(self.__dict__[errorstring])             # <<<<<<<<<<<<<<
@@ -18799,14 +19028,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34warnerror(PyObject *__pyx_self, PyObject
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-      __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+      __Pyx_GOTREF(__pyx_t_1);
       PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3);
       __Pyx_GIVEREF(__pyx_t_3);
       __pyx_t_3 = 0;
-      __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 936; __pyx_clineno = __LINE__; goto __pyx_L6_error;}
+      __pyx_t_3 = PyObject_Call(__pyx_t_2, __pyx_t_1, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 936; __pyx_clineno = __LINE__; goto __pyx_L6_error;}
       __Pyx_GOTREF(__pyx_t_3);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-      __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
       __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
     }
     __Pyx_XDECREF(__pyx_save_exc_type); __pyx_save_exc_type = 0;
@@ -18818,7 +19047,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34warnerror(PyObject *__pyx_self, PyObject
     __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
     __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-    /* "cvcf.pyx":937
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":937
  *     def warnerror(self, errorstring):
  *         try:             self._warn_errors.add(self.__dict__[errorstring])
  *         except KeyError: raise ValueError("Invalid error string: %s" % errorstring)             # <<<<<<<<<<<<<<
@@ -18832,16 +19061,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34warnerror(PyObject *__pyx_self, PyObject
       __Pyx_GOTREF(__pyx_t_3);
       __Pyx_GOTREF(__pyx_t_1);
       __Pyx_GOTREF(__pyx_t_2);
-      __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_121), __pyx_v_errorstring); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;}
+      __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_71), __pyx_v_errorstring); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;}
       __Pyx_GOTREF(((PyObject *)__pyx_t_5));
       __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;}
-      __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+      __Pyx_GOTREF(__pyx_t_6);
       PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_5));
       __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
       __pyx_t_5 = 0;
-      __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;}
+      __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;}
       __Pyx_GOTREF(__pyx_t_5);
-      __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
       __Pyx_Raise(__pyx_t_5, 0, 0);
       __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
       {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;}
@@ -18880,7 +19109,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34warnerror(PyObject *__pyx_self, PyObject
   return __pyx_r;
 }
 
-/* "cvcf.pyx":939
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":939
  *         except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
  * 
  *     def parse(self, stream):             # <<<<<<<<<<<<<<
@@ -18888,10 +19117,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34warnerror(PyObject *__pyx_self, PyObject
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  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_35parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_35parse[] = " Parse a stream of VCF-formatted lines.  Initializes class instance and return generator ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_35parse = {__Pyx_NAMESTR("parse"), (PyCFunction)__pyx_pf_4cvcf_3VCF_35parse, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_35parse)};
-static PyObject *__pyx_pf_4cvcf_3VCF_35parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_parse[] = " Parse a stream of VCF-formatted lines.  Initializes class instance and return generator ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_parse = {__Pyx_NAMESTR("parse"), (PyCFunction)__pyx_pf_4cvcf_3VCF_parse, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_parse)};
+static PyObject *__pyx_pf_4cvcf_3VCF_parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_stream = 0;
   PyObject *__pyx_v_last_line;
@@ -18944,7 +19173,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_35parse(PyObject *__pyx_self, PyObject *__p
   __pyx_L4_argument_unpacking_done:;
   __pyx_v_last_line = Py_None; __Pyx_INCREF(Py_None);
 
-  /* "cvcf.pyx":941
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":941
  *     def parse(self, stream):
  *         """ Parse a stream of VCF-formatted lines.  Initializes class instance and return generator """
  *         last_line = self._parse_header(stream)             # <<<<<<<<<<<<<<
@@ -18954,19 +19183,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_35parse(PyObject *__pyx_self, PyObject *__p
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   __Pyx_GOTREF(__pyx_t_1);
   __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+  __Pyx_GOTREF(__pyx_t_2);
   __Pyx_INCREF(__pyx_v_stream);
   PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stream);
   __Pyx_GIVEREF(__pyx_v_stream);
-  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_v_last_line);
   __pyx_v_last_line = __pyx_t_3;
   __pyx_t_3 = 0;
 
-  /* "cvcf.pyx":944
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":944
  *         # 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)             # <<<<<<<<<<<<<<
@@ -18977,17 +19206,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_35parse(PyObject *__pyx_self, PyObject *__p
   __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parse); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
   __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+  __Pyx_GOTREF(__pyx_t_2);
   __Pyx_INCREF(__pyx_v_last_line);
   PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_last_line);
   __Pyx_GIVEREF(__pyx_v_last_line);
   __Pyx_INCREF(__pyx_v_stream);
   PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_stream);
   __Pyx_GIVEREF(__pyx_v_stream);
-  __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(__pyx_t_3, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __pyx_r = __pyx_t_1;
   __pyx_t_1 = 0;
   goto __pyx_L0;
@@ -19007,7 +19236,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_35parse(PyObject *__pyx_self, PyObject *__p
   return __pyx_r;
 }
 
-/* "cvcf.pyx":946
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":946
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  * 
  *     def write(self, stream, datagenerator):             # <<<<<<<<<<<<<<
@@ -19015,10 +19244,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_35parse(PyObject *__pyx_self, PyObject *__p
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  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_36write(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_36write[] = " Writes a VCF file to a stream, using a data generator (or list) ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_36write = {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_4cvcf_3VCF_36write, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_36write)};
-static PyObject *__pyx_pf_4cvcf_3VCF_36write(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_write(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_write[] = " Writes a VCF file to a stream, using a data generator (or list) ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_write = {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_4cvcf_3VCF_write, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_write)};
+static PyObject *__pyx_pf_4cvcf_3VCF_write(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_stream = 0;
   PyObject *__pyx_v_datagenerator = 0;
@@ -19083,7 +19312,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36write(PyObject *__pyx_self, PyObject *__p
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   __pyx_v_data = Py_None; __Pyx_INCREF(Py_None);
 
-  /* "cvcf.pyx":948
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":948
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  *         self.write_header(stream)             # <<<<<<<<<<<<<<
@@ -19093,17 +19322,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36write(PyObject *__pyx_self, PyObject *__p
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+  __Pyx_GOTREF(__pyx_t_2);
   __Pyx_INCREF(__pyx_v_stream);
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   __Pyx_GIVEREF(__pyx_v_stream);
-  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "cvcf.pyx":949
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":949
  *         """ Writes a VCF file to a stream, using a data generator (or list) """
  *         self.write_header(stream)
  *         self.write_heading(stream)             # <<<<<<<<<<<<<<
@@ -19113,17 +19342,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36write(PyObject *__pyx_self, PyObject *__p
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+  __Pyx_GOTREF(__pyx_t_2);
   __Pyx_INCREF(__pyx_v_stream);
   PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stream);
   __Pyx_GIVEREF(__pyx_v_stream);
-  __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(__pyx_t_3, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "cvcf.pyx":950
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":950
  *         self.write_header(stream)
  *         self.write_heading(stream)
  *         for data in datagenerator: self.write_data(stream,data)             # <<<<<<<<<<<<<<
@@ -19157,17 +19386,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36write(PyObject *__pyx_self, PyObject *__p
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-    __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+    __Pyx_GOTREF(__pyx_t_3);
     __Pyx_INCREF(__pyx_v_stream);
     PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stream);
     __Pyx_GIVEREF(__pyx_v_stream);
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     PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_data);
     __Pyx_GIVEREF(__pyx_v_data);
-    __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 950; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_5 = PyObject_Call(__pyx_t_2, __pyx_t_3, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 950; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-    __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
     __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
   }
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -19188,7 +19417,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36write(PyObject *__pyx_self, PyObject *__p
   return __pyx_r;
 }
 
-/* "cvcf.pyx":952
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":952
  *         for data in datagenerator: self.write_data(stream,data)
  * 
  *     def writeheader(self, stream):             # <<<<<<<<<<<<<<
@@ -19196,10 +19425,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36write(PyObject *__pyx_self, PyObject *__p
  *         self.write_header(stream)
  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_37writeheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_37writeheader[] = " Writes a VCF header ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_37writeheader = {__Pyx_NAMESTR("writeheader"), (PyCFunction)__pyx_pf_4cvcf_3VCF_37writeheader, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_37writeheader)};
-static PyObject *__pyx_pf_4cvcf_3VCF_37writeheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_writeheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_writeheader[] = " Writes a VCF header ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_writeheader = {__Pyx_NAMESTR("writeheader"), (PyCFunction)__pyx_pf_4cvcf_3VCF_writeheader, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_writeheader)};
+static PyObject *__pyx_pf_4cvcf_3VCF_writeheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_stream = 0;
   PyObject *__pyx_r = NULL;
@@ -19250,7 +19479,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_37writeheader(PyObject *__pyx_self, PyObjec
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":954
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":954
  *     def writeheader(self, stream):
  *         """ Writes a VCF header """
  *         self.write_header(stream)             # <<<<<<<<<<<<<<
@@ -19260,17 +19489,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_37writeheader(PyObject *__pyx_self, PyObjec
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+  __Pyx_GOTREF(__pyx_t_2);
   __Pyx_INCREF(__pyx_v_stream);
   PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stream);
   __Pyx_GIVEREF(__pyx_v_stream);
-  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "cvcf.pyx":955
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":955
  *         """ Writes a VCF header """
  *         self.write_header(stream)
  *         self.write_heading(stream)             # <<<<<<<<<<<<<<
@@ -19280,14 +19509,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_37writeheader(PyObject *__pyx_self, PyObjec
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+  __Pyx_GOTREF(__pyx_t_2);
   __Pyx_INCREF(__pyx_v_stream);
   PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stream);
   __Pyx_GIVEREF(__pyx_v_stream);
-  __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 955; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(__pyx_t_3, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 955; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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   __pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -19304,7 +19533,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_37writeheader(PyObject *__pyx_self, PyObjec
   return __pyx_r;
 }
 
-/* "cvcf.pyx":957
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":957
  *         self.write_heading(stream)
  * 
  *     def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2):             # <<<<<<<<<<<<<<
@@ -19312,10 +19541,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_37writeheader(PyObject *__pyx_self, PyObjec
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-static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_38compare_calls[] = " Utility function: compares two calls for equality ";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_38compare_calls = {__Pyx_NAMESTR("compare_calls"), (PyCFunction)__pyx_pf_4cvcf_3VCF_38compare_calls, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_38compare_calls)};
-static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_compare_calls(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_compare_calls[] = " Utility function: compares two calls for equality ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_compare_calls = {__Pyx_NAMESTR("compare_calls"), (PyCFunction)__pyx_pf_4cvcf_3VCF_compare_calls, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_compare_calls)};
+static PyObject *__pyx_pf_4cvcf_3VCF_compare_calls(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_pos1 = 0;
   PyObject *__pyx_v_ref1 = 0;
@@ -19425,7 +19654,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObj
   __Pyx_INCREF(__pyx_v_ref2);
   __Pyx_INCREF(__pyx_v_alt2);
 
-  /* "cvcf.pyx":962
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":962
  *         # 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             # <<<<<<<<<<<<<<
@@ -19447,7 +19676,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObj
   }
   __pyx_L6:;
 
-  /* "cvcf.pyx":965
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":965
  *         # 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]:             # <<<<<<<<<<<<<<
@@ -19481,34 +19710,34 @@ static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObj
     }
     if (!__pyx_t_4) break;
 
-    /* "cvcf.pyx":966
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":966
  *         # 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]:
  */
-    __pyx_t_6 = __Pyx_PySequence_GetSlice(__pyx_v_ref1, 0, -1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 966; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_6 = PySequence_GetSlice(__pyx_v_ref1, 0, -1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 966; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     __Pyx_DECREF(__pyx_v_ref1);
     __pyx_v_ref1 = __pyx_t_6;
     __pyx_t_6 = 0;
 
-    /* "cvcf.pyx":967
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":967
  *         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]
  */
-    __pyx_t_6 = __Pyx_PySequence_GetSlice(__pyx_v_alt1, 0, -1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_6 = PySequence_GetSlice(__pyx_v_alt1, 0, -1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_6);
     __Pyx_DECREF(__pyx_v_alt1);
     __pyx_v_alt1 = __pyx_t_6;
     __pyx_t_6 = 0;
   }
 
-  /* "cvcf.pyx":968
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":968
  *             ref1 = ref1[:-1]
  *             alt1 = alt1[:-1]
  *         while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:             # <<<<<<<<<<<<<<
@@ -19542,34 +19771,34 @@ static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObj
     }
     if (!__pyx_t_2) break;
 
-    /* "cvcf.pyx":969
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":969
  *             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
  */
-    __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_ref2, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_1 = PySequence_GetSlice(__pyx_v_ref2, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_1);
     __Pyx_DECREF(__pyx_v_ref2);
     __pyx_v_ref2 = __pyx_t_1;
     __pyx_t_1 = 0;
 
-    /* "cvcf.pyx":970
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":970
  *         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
  */
-    __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_alt2, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_1 = PySequence_GetSlice(__pyx_v_alt2, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_1);
     __Pyx_DECREF(__pyx_v_alt2);
     __pyx_v_alt2 = __pyx_t_1;
     __pyx_t_1 = 0;
   }
 
-  /* "cvcf.pyx":972
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":972
  *             alt2 = alt2[:-1]
  *         # now, the alternative alleles must be identical
  *         return alt1 == alt2             # <<<<<<<<<<<<<<
@@ -19601,7 +19830,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObj
   return __pyx_r;
 }
 
-/* "cvcf.pyx":979
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":979
  * ###########################################################################################################
  * 
  *     def connect( self, filename ):             # <<<<<<<<<<<<<<
@@ -19609,10 +19838,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObj
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  */
 
-static PyObject *__pyx_pf_4cvcf_3VCF_39connect(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_4cvcf_3VCF_39connect[] = "connect to tabix file.";
-static PyMethodDef __pyx_mdef_4cvcf_3VCF_39connect = {__Pyx_NAMESTR("connect"), (PyCFunction)__pyx_pf_4cvcf_3VCF_39connect, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_39connect)};
-static PyObject *__pyx_pf_4cvcf_3VCF_39connect(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_connect(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_connect[] = "connect to tabix file.";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_connect = {__Pyx_NAMESTR("connect"), (PyCFunction)__pyx_pf_4cvcf_3VCF_connect, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_connect)};
+static PyObject *__pyx_pf_4cvcf_3VCF_connect(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
   PyObject *__pyx_v_filename = 0;
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@@ -19663,7 +19892,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_39connect(PyObject *__pyx_self, PyObject *_
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":981
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":981
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@@ -19676,18 +19905,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_39connect(PyObject *__pyx_self, PyObject *_
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+  __Pyx_GOTREF(__pyx_t_1);
   __Pyx_INCREF(__pyx_v_filename);
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-  __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(__pyx_t_2, __pyx_t_1, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__tabixfile, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "cvcf.pyx":982
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":982
  *         '''connect to tabix file.'''
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  *         self._parse_header(self.tabixfile.header)             # <<<<<<<<<<<<<<
@@ -19702,14 +19931,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_39connect(PyObject *__pyx_self, PyObject *_
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+  __Pyx_GOTREF(__pyx_t_1);
   PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
   __Pyx_GIVEREF(__pyx_t_2);
   __pyx_t_2 = 0;
-  __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 982; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyObject_Call(__pyx_t_3, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 982; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
   __pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -19726,7 +19955,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_39connect(PyObject *__pyx_self, PyObject *_
   return __pyx_r;
 }
 
-/* "cvcf.pyx":984
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":984
  *         self._parse_header(self.tabixfile.header)
  * 
  *     def fetch(self,             # <<<<<<<<<<<<<<
@@ -19734,10 +19963,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_39connect(PyObject *__pyx_self, PyObject *_
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-static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_fetch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_fetch[] = " Parse a stream of VCF-formatted lines.  Initializes class instance and return generator ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_fetch = {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_4cvcf_3VCF_fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_fetch)};
+static PyObject *__pyx_pf_4cvcf_3VCF_fetch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_self = 0;
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   PyObject *__pyx_v_start = 0;
@@ -19756,7 +19985,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p
     Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
     PyObject* values[5] = {0,0,0,0,0};
 
-    /* "cvcf.pyx":985
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":985
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  *     def fetch(self,
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@@ -19765,7 +19994,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p
  */
     values[1] = ((PyObject *)Py_None);
 
-    /* "cvcf.pyx":986
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":986
  *     def fetch(self,
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  *               start = None,             # <<<<<<<<<<<<<<
@@ -19774,7 +20003,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p
  */
     values[2] = ((PyObject *)Py_None);
 
-    /* "cvcf.pyx":987
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":987
  *               reference = None,
  *               start = None,
  *               end = None,             # <<<<<<<<<<<<<<
@@ -19783,7 +20012,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p
  */
     values[3] = ((PyObject *)Py_None);
 
-    /* "cvcf.pyx":988
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":988
  *               start = None,
  *               end = None,
  *               region = None ):             # <<<<<<<<<<<<<<
@@ -19836,7 +20065,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p
     __pyx_v_region = values[4];
   } else {
 
-    /* "cvcf.pyx":985
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":985
  * 
  *     def fetch(self,
  *               reference = None,             # <<<<<<<<<<<<<<
@@ -19845,7 +20074,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p
  */
     __pyx_v_reference = ((PyObject *)Py_None);
 
-    /* "cvcf.pyx":986
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":986
  *     def fetch(self,
  *               reference = None,
  *               start = None,             # <<<<<<<<<<<<<<
@@ -19854,7 +20083,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p
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-    /* "cvcf.pyx":987
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":987
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  *               start = None,
  *               end = None,             # <<<<<<<<<<<<<<
@@ -19863,7 +20092,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p
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     __pyx_v_end = ((PyObject *)Py_None);
 
-    /* "cvcf.pyx":988
+    /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":988
  *               start = None,
  *               end = None,
  *               region = None ):             # <<<<<<<<<<<<<<
@@ -19890,7 +20119,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p
   return NULL;
   __pyx_L4_argument_unpacking_done:;
 
-  /* "cvcf.pyx":991
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":991
  *         """ Parse a stream of VCF-formatted lines.  Initializes class instance and return generator """
  * 
  *         return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord( self ) )             # <<<<<<<<<<<<<<
@@ -19904,7 +20133,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+  __Pyx_GOTREF(__pyx_t_1);
   __Pyx_INCREF(__pyx_v_reference);
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@@ -19920,19 +20149,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+  __Pyx_GOTREF(__pyx_t_4);
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+  __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_4cvcf_asVCFRecord)), __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 991; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+  __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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+  __pyx_t_5 = PyEval_CallObjectWithKeywords(__pyx_t_2, __pyx_t_1, ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 991; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-  __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
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@@ -19954,7 +20183,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p
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 }
 
-/* "cvcf.pyx":993
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  * 
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@@ -19962,10 +20191,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p
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-static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pf_4cvcf_3VCF_validate(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_4cvcf_3VCF_validate[] = "validate vcf record.\n\n        returns a validated record.\n        ";
+static PyMethodDef __pyx_mdef_4cvcf_3VCF_validate = {__Pyx_NAMESTR("validate"), (PyCFunction)__pyx_pf_4cvcf_3VCF_validate, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_validate)};
+static PyObject *__pyx_pf_4cvcf_3VCF_validate(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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   PyObject *__pyx_v_record = 0;
   PyObject *__pyx_v_chrom;
@@ -19990,6 +20219,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject *
   int __pyx_v_movable;
   PyObject *__pyx_v_longest;
   PyObject *__pyx_v_shortest;
+  PyObject *__pyx_8genexpr1__pyx_v_allele;
   PyObject *__pyx_r = NULL;
   PyObject *__pyx_t_1 = NULL;
   PyObject *__pyx_t_2 = NULL;
@@ -20061,156 +20291,163 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject *
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   __pyx_v_faref = Py_None; __Pyx_INCREF(Py_None);
   __pyx_v_f = Py_None; __Pyx_INCREF(Py_None);
-  __pyx_v_newalts = ((PyObject*)Py_None); __Pyx_INCREF(Py_None);
+  __pyx_v_newalts = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
   __pyx_v_a = Py_None; __Pyx_INCREF(Py_None);
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   __pyx_v_na = Py_None; __Pyx_INCREF(Py_None);
   __pyx_v_s = Py_None; __Pyx_INCREF(Py_None);
-  __pyx_v_alt = ((PyObject*)Py_None); __Pyx_INCREF(Py_None);
+  __pyx_v_alt = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
   __pyx_v_addn = Py_None; __Pyx_INCREF(Py_None);
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   __pyx_v_longest = Py_None; __Pyx_INCREF(Py_None);
   __pyx_v_shortest = Py_None; __Pyx_INCREF(Py_None);
+  __pyx_8genexpr1__pyx_v_allele = Py_None; __Pyx_INCREF(Py_None);
 
-  /* "cvcf.pyx":999
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":999
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-  __pyx_t_1 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_123), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
-  __Pyx_Raise(__pyx_t_1, 0, 0);
+  __Pyx_INCREF(((PyObject *)__pyx_kp_s_72));
+  PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_72));
+  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_72));
+  __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_2);
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+  __Pyx_Raise(__pyx_t_2, 0, 0);
+  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "cvcf.pyx":1001
+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":1001
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  * 
  *         chrom, pos = record.chrom, record.pos             # <<<<<<<<<<<<<<
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-              /* "cvcf.pyx":1048
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-        __Pyx_GOTREF(((PyObject *)__pyx_t_10));
+        __Pyx_GOTREF(__pyx_t_10);
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-        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-        __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
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-      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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-        PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_t_1);
-        __Pyx_GIVEREF(__pyx_t_1);
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-        __pyx_t_5 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_6); __Pyx_INCREF(__pyx_t_5); __pyx_t_6++;
+        if (__pyx_t_6 >= PyList_GET_SIZE(__pyx_t_2)) break;
+        __pyx_t_5 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_5); __pyx_t_6++;
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-        /* "cvcf.pyx":1101
+        /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":1101
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@@ -22143,7 +22398,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject *
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-          /* "cvcf.pyx":1102
+          /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":1102
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@@ -22160,11 +22415,11 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject *
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           __pyx_t_13 = 0;
-          goto __pyx_L72;
+          goto __pyx_L68;
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         /*else*/ {
 
-          /* "cvcf.pyx":1104
+          /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":1104
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@@ -22182,9 +22437,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject *
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           __pyx_t_5 = 0;
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-        __pyx_L72:;
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-        /* "cvcf.pyx":1105
+        /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":1105
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+          __pyx_t_5 = PySequence_GetSlice(__pyx_v_longest, 0, __pyx_t_8); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1105; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+          goto __pyx_L69;
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-          goto __pyx_L74;
+          goto __pyx_L70;
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-      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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-        /* "cvcf.pyx":1110
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-        goto __pyx_L75;
+        goto __pyx_L65_break;
+        goto __pyx_L71;
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-      __pyx_L75:;
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-      /* "cvcf.pyx":1111
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-      __Pyx_GOTREF(__pyx_t_1);
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-      __pyx_v_ref = __pyx_t_1;
-      __pyx_t_1 = 0;
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-      /* "cvcf.pyx":1112
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-      __Pyx_INCREF(((PyObject *)__pyx_t_1));
+      __Pyx_INCREF(((PyObject *)__pyx_t_2));
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-      __pyx_v_alt = __pyx_t_1;
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-      /* "cvcf.pyx":1113
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       __Pyx_GOTREF(__pyx_t_5);
-      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+      PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_2));
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+      __Pyx_GOTREF(__pyx_t_2);
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+      __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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@@ -22394,7 +22651,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject *
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-        /* "cvcf.pyx":1114
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-        __Pyx_GOTREF(__pyx_t_1);
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-        __pyx_t_1 = 0;
+        __pyx_v_ref = __pyx_t_2;
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-        /* "cvcf.pyx":1115
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+        __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+        if (likely(((PyObject *)__pyx_v_alt) != Py_None)) {
+          __pyx_t_6 = 0; __pyx_t_5 = ((PyObject *)__pyx_v_alt); __Pyx_INCREF(__pyx_t_5);
+        } else {
+          PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -22446,35 +22704,35 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject *
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         }
         __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
-        __Pyx_INCREF(((PyObject *)__pyx_t_1));
+        __Pyx_INCREF(((PyObject *)__pyx_t_2));
         __Pyx_DECREF(((PyObject *)__pyx_v_alt));
-        __pyx_v_alt = __pyx_t_1;
-        __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+        __pyx_v_alt = __pyx_t_2;
+        __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
 
-        /* "cvcf.pyx":1116
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  *                     alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
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-        __Pyx_GOTREF(__pyx_t_1);
+        __pyx_t_2 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __Pyx_GOTREF(__pyx_t_2);
         __Pyx_DECREF(__pyx_v_pos);
-        __pyx_v_pos = __pyx_t_1;
-        __pyx_t_1 = 0;
-        goto __pyx_L78;
+        __pyx_v_pos = __pyx_t_2;
+        __pyx_t_2 = 0;
+        goto __pyx_L74;
       }
-      __pyx_L78:;
+      __pyx_L74:;
     }
-    __pyx_L69_break:;
-    goto __pyx_L67;
+    __pyx_L65_break:;
+    goto __pyx_L63;
   }
-  __pyx_L67:;
+  __pyx_L63:;
 
   __pyx_r = Py_None; __Pyx_INCREF(Py_None);
   goto __pyx_L0;
@@ -22513,6 +22771,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject *
   __Pyx_DECREF(__pyx_v_allele);
   __Pyx_DECREF(__pyx_v_longest);
   __Pyx_DECREF(__pyx_v_shortest);
+  __Pyx_DECREF(__pyx_8genexpr1__pyx_v_allele);
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   __Pyx_RefNannyFinishContext();
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@@ -22526,7 +22785,7 @@ static PyObject *__pyx_tp_new_4cvcf_VCFRecord(PyTypeObject *t, PyObject *a, PyOb
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   p->vcf = Py_None; Py_INCREF(Py_None);
-  if (__pyx_pf_4cvcf_9VCFRecord_1__cinit__(o, a, k) < 0) {
+  if (__pyx_pf_4cvcf_9VCFRecord___cinit__(o, a, k) < 0) {
     Py_DECREF(o); o = 0;
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   return o;
@@ -22686,7 +22945,7 @@ static PyNumberMethods __pyx_tp_as_number_VCFRecord = {
 };
 
 static PySequenceMethods __pyx_tp_as_sequence_VCFRecord = {
-  __pyx_pf_4cvcf_9VCFRecord_2__len__, /*sq_length*/
+  __pyx_pf_4cvcf_9VCFRecord___len__, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
   __pyx_sq_item_4cvcf_VCFRecord, /*sq_item*/
@@ -22699,8 +22958,8 @@ static PySequenceMethods __pyx_tp_as_sequence_VCFRecord = {
 };
 
 static PyMappingMethods __pyx_tp_as_mapping_VCFRecord = {
-  __pyx_pf_4cvcf_9VCFRecord_2__len__, /*mp_length*/
-  __pyx_pf_4cvcf_9VCFRecord_3__getitem__, /*mp_subscript*/
+  __pyx_pf_4cvcf_9VCFRecord___len__, /*mp_length*/
+  __pyx_pf_4cvcf_9VCFRecord___getitem__, /*mp_subscript*/
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 };
 
@@ -22725,7 +22984,7 @@ static PyBufferProcs __pyx_tp_as_buffer_VCFRecord = {
   #endif
 };
 
-static PyTypeObject __pyx_type_4cvcf_VCFRecord = {
+PyTypeObject __pyx_type_4cvcf_VCFRecord = {
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   __Pyx_NAMESTR("cvcf.VCFRecord"), /*tp_name*/
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@@ -22749,7 +23008,7 @@ static PyTypeObject __pyx_type_4cvcf_VCFRecord = {
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   0, /*tp_setattro*/
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-  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   __Pyx_DOCSTR("vcf record.\n\n    initialized from data and vcf meta \n    "), /*tp_doc*/
   __pyx_tp_traverse_4cvcf_VCFRecord, /*tp_traverse*/
   __pyx_tp_clear_4cvcf_VCFRecord, /*tp_clear*/
@@ -22922,7 +23181,7 @@ static PyBufferProcs __pyx_tp_as_buffer_asVCFRecord = {
   #endif
 };
 
-static PyTypeObject __pyx_type_4cvcf_asVCFRecord = {
+PyTypeObject __pyx_type_4cvcf_asVCFRecord = {
   PyVarObject_HEAD_INIT(0, 0)
   __Pyx_NAMESTR("cvcf.asVCFRecord"), /*tp_name*/
   sizeof(struct __pyx_obj_4cvcf_asVCFRecord), /*tp_basicsize*/
@@ -22941,12 +23200,12 @@ static PyTypeObject __pyx_type_4cvcf_asVCFRecord = {
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   &__pyx_tp_as_mapping_asVCFRecord, /*tp_as_mapping*/
   0, /*tp_hash*/
-  __pyx_pf_4cvcf_11asVCFRecord_1__call__, /*tp_call*/
+  __pyx_pf_4cvcf_11asVCFRecord___call__, /*tp_call*/
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   0, /*tp_getattro*/
   0, /*tp_setattro*/
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-  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   __Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record."), /*tp_doc*/
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@@ -22979,6 +23238,8 @@ static PyTypeObject __pyx_type_4cvcf_asVCFRecord = {
 };
 
 static PyMethodDef __pyx_methods[] = {
+  {__Pyx_NAMESTR("get_sequence"), (PyCFunction)__pyx_pf_4cvcf_get_sequence, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("parse_regions"), (PyCFunction)__pyx_pf_4cvcf_parse_regions, METH_O, __Pyx_DOCSTR(0)},
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 };
 
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+  __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;};
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-  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_7));
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+PyMODINIT_FUNC initcvcf(void); /*proto*/
+PyMODINIT_FUNC initcvcf(void)
+#else
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+PyMODINIT_FUNC PyInit_cvcf(void)
+#endif
+{
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+  PyEval_InitThreads();
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+  Py_INCREF(__pyx_m);
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+  /*--- Function export code ---*/
+  /*--- Type init code ---*/
+  __pyx_ptype_10TabProxies_TupleProxy = __Pyx_ImportType("TabProxies", "TupleProxy", sizeof(struct __pyx_obj_10TabProxies_TupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":46
+ * #
  * 
+ * from collections import namedtuple, defaultdict             # <<<<<<<<<<<<<<
+ * from operator import itemgetter
+ * import sys, re, copy, bisect
  */
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+  /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":48
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-  /* "cvcf.pyx":52
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+  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+  __pyx_t_2 = PyObject_GetAttr(__pyx_m, __pyx_n_s__VCF); 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 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__connect); 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;
+  __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_122), __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__VCF); 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 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__fetch); 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;
+  __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_123), __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__VCF); 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 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__validate); 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;
+  __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_124), __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;
+  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;
 
-  /* "ctabix.pxd":2
+  /* "pysam/ctabix.pxd":2
  * 
  * cdef extern from "string.h":             # <<<<<<<<<<<<<<
  *   ctypedef int size_t
@@ -25287,6 +25113,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
   __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;
@@ -25312,6 +25139,19 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
     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,
@@ -25342,19 +25182,6 @@ static void __Pyx_RaiseArgtupleInvalid(
         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[],
@@ -25413,210 +25240,73 @@ static int __Pyx_ParseOptionalKeywords(
             }
         }
     }
-    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 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;
+    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;
 }
 
-#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");
+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 (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");
+    #if PY_MAJOR_VERSION >= 3
+    if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
         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);
-        }
-    }
-
+    #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:
-    return;
+    *type = 0;
+    *value = 0;
+    *tb = 0;
+    Py_XDECREF(local_type);
+    Py_XDECREF(local_value);
+    Py_XDECREF(local_tb);
+    return -1;
 }
-#endif
+
 
 static double __Pyx__PyObject_AsDouble(PyObject* obj) {
     PyObject* float_value;
@@ -25756,91 +25446,167 @@ bad:
     return module;
 }
 
-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 PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
-                                   PyObject *modname) {
-    PyObject *result;
-    PyObject *metaclass;
-
-    if (PyDict_SetItemString(dict, "__module__", modname) < 0)
-        return NULL;
+static PyObject *__Pyx_CreateClass(
+    PyObject *bases, PyObject *dict, PyObject *name, const char *modname)
+{
+    PyObject *py_modname;
+    PyObject *result = 0;
 
-    /* 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);
+    #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();
 
-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;
+    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 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);
+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_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) {
-       if (obj == Py_None)
-               obj = NULL;
-       return PyMethod_New(func, obj, type);
+
+#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;
 }
 
-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;
+#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;
     }
-    __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type;
-    return 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;
+    }
+
+    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;
@@ -26295,13 +26061,13 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
     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
@@ -26311,7 +26077,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
         #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;
@@ -26346,23 +26112,22 @@ bad:
 }
 #endif
 
-static void* __Pyx_GetVtable(PyObject *dict) {
-    void* ptr;
+static int __Pyx_GetVtable(PyObject *dict, void *vtabptr) {
     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)
-    ptr = PyCapsule_GetPointer(ob, 0);
+    *(void **)vtabptr = PyCapsule_GetPointer(ob, 0);
 #else
-    ptr = PyCObject_AsVoidPtr(ob);
+    *(void **)vtabptr = PyCObject_AsVoidPtr(ob);
 #endif
-    if (!ptr && !PyErr_Occurred())
-        PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
+    if (!*(void **)vtabptr)
+        goto bad;
     Py_DECREF(ob);
-    return ptr;
+    return 0;
 bad:
     Py_XDECREF(ob);
-    return NULL;
+    return -1;
 }
 
 static int __Pyx_SetVtable(PyObject *dict, void *vtable) {