X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=pysam%2Fcsamtools.pxd;h=4ec74e3693c86aea8cc7052db6ace9a770c6bb6d;hp=b614a844fa8cb9d75ef33cdef7a11a6c81d2e1ad;hb=ca46ef4ba4a883c57cea62d5bf1bc021f1185109;hpb=6a7c3f175b210cc16d09a5e8e4c1d47333dbe1c6

diff --git a/pysam/csamtools.pxd b/pysam/csamtools.pxd
index b614a84..4ec74e3 100644
--- a/pysam/csamtools.pxd
+++ b/pysam/csamtools.pxd
@@ -1,4 +1,3 @@
-
 cdef extern from "string.h":
   ctypedef int size_t
   void *memcpy(void *dst,void *src,size_t len)
@@ -14,6 +13,9 @@ cdef extern from "stdlib.h":
   void qsort(void *base, size_t nmemb, size_t size,
              int (*compar)(void *,void *))
 
+cdef extern from "math.h":
+   double sqrt(double x)
+
 cdef extern from "stdio.h":
   ctypedef struct FILE:
     pass
@@ -52,6 +54,11 @@ cdef extern from "string.h":
 
 cdef extern from "Python.h":
    long _Py_HashPointer(void*)
+   FILE* PyFile_AsFile(object)
+
+cdef extern from "fileobject.h":
+   ctypedef class __builtin__.file [object PyFileObject]:
+        pass
 
 cdef extern from "razf.h":
   pass
@@ -63,9 +70,10 @@ cdef extern from "stdint.h":
   ctypedef int uint8_t
   ctypedef int uint64_t
 
-
 cdef extern from "bam.h":
 
+  # constants
+  int BAM_DEF_MASK
   # IF _IOLIB=2, bamFile = BGZF, see bgzf.h
   # samtools uses KNETFILE, check how this works
 
@@ -118,13 +126,22 @@ cdef extern from "bam.h":
      char *text
 
   ctypedef struct bam_index_t:
-      pass
+      int32_t n
+      uint64_t n_no_coor
 
   ctypedef struct bam_plbuf_t:
       pass
 
+  ctypedef struct pair64_t:
+      uint64_t u, v
+      
   ctypedef struct bam_iter_t:
-      pass
+      int from_first
+      int tid, beg, end, n_off, i, finished
+      uint64_t curr_off
+      pair64_t *off
+
+  # ctypedef __bam_iter_t * bam_iter_t
 
   bam1_t * bam_init1()
   void bam_destroy1(bam1_t *)
@@ -176,20 +193,23 @@ cdef extern from "bam.h":
   ctypedef struct bam_plp_t:
       pass
 
+  ctypedef bam_pileup1_t * const_bam_pileup1_t_ptr "const bam_pileup1_t *"
+
   ctypedef int (*bam_plp_auto_f)(void *data, bam1_t *b)
 
   bam_plp_t bam_plp_init( bam_plp_auto_f func, void *data)
   int bam_plp_push( bam_plp_t iter,  bam1_t *b)
-  bam_pileup1_t *bam_plp_next( bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
-  bam_pileup1_t *bam_plp_auto( bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
+  bam_pileup1_t * bam_plp_next( bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
+  bam_pileup1_t * bam_plp_auto( bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
   void bam_plp_set_mask(bam_plp_t iter, int mask)
   void bam_plp_reset(bam_plp_t iter)
   void bam_plp_destroy(bam_plp_t iter)
+  void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt)
 
   ##################################################
 
-  int bam_read1(bamFile fp, bam1_t *b)
-
+  int bam_read1( bamFile fp, bam1_t *b)
+  int bam_validate1( bam_header_t *header, bam1_t *b)
   int bam_write1( bamFile fp, bam1_t *b)
 
   bam_header_t *bam_header_init()
@@ -206,7 +226,7 @@ cdef extern from "bam.h":
 
   uint8_t *bam_aux_get(bam1_t *b,  char tag[2])
 
-  int bam_aux2i(uint8_t *s)
+  int32_t bam_aux2i(uint8_t *s)
   float bam_aux2f(uint8_t *s)
   double bam_aux2d(uint8_t *s)
   char bam_aux2A( uint8_t *s)
@@ -216,6 +236,9 @@ cdef extern from "bam.h":
 
   uint32_t bam_calend(bam1_core_t *c, uint32_t *cigar)
 
+cdef extern from *:
+    ctypedef char* const_char_ptr "const char*"
+
 cdef extern from "sam.h":
 
   ctypedef struct samfile_t_un:
@@ -228,7 +251,7 @@ cdef extern from "sam.h":
      samfile_t_un x
      bam_header_t *header
 
-  samfile_t *samopen( char *fn, char * mode, void *aux)
+  samfile_t *samopen( const_char_ptr fn, char * mode, void *aux)
 
   int sampileup( samfile_t *fp, int mask, bam_pileup_f func, void *data)
 
@@ -238,6 +261,73 @@ cdef extern from "sam.h":
 
   int samwrite(samfile_t *fp, bam1_t *b)
 
+  int bam_prob_realn(bam1_t *b, char *ref)
+  int bam_cap_mapQ(bam1_t *b, char *ref, int thres)
+
+
+#cdef extern from "glf.h":
+#   ctypedef struct glf1_t:
+#      pass
+
+#cdef extern from "bam_maqcns.h":
+#
+#  ctypedef struct bam_maqcns_t:
+#     float het_rate, theta
+#     int n_hap, cap_mapQ, errmod, min_baseQ
+#     float eta, q_r
+#     double *fk, *coef
+#     double *lhet
+#     void *aux
+
+#  glf1_t *bam_maqcns_glfgen(int n, 
+#                            bam_pileup1_t *pl, 
+#                            uint8_t ref_base, 
+#                            bam_maqcns_t *bm)
+
+#  ctypedef struct bam_maqindel_opt_t:
+#      int q_indel
+#      float r_indel
+#      float r_snp
+#      int mm_penalty, indel_err, ambi_thres
+     
+#  uint32_t bam_maqcns_call(int n, bam_pileup1_t *pl, bam_maqcns_t *bm)
+#  bam_maqcns_t * bam_maqcns_init()
+#  void bam_maqcns_destroy(bam_maqcns_t *bm)
+#  void bam_maqcns_prepare(bam_maqcns_t *bm)
+  
+#  uint32_t glf2cns(glf1_t *g, int q_r)
+
+#  int BAM_ERRMOD_MAQ2
+#  int BAM_ERRMOD_MAQ
+#  int BAM_ERRMOD_SOAP
+
+#  ctypedef struct bam_maqindel_ret_t: 
+#    int indel1
+#    int indel2        
+#    int cnt1
+#    int cnt2
+#    int cnt_anti
+#    int cnt_ref
+#    int cnt_ambi
+#    char *s[2]
+#    int gt
+#    int gl[2]
+#    int q_cns
+#    int q_ref
+    
+#  void bam_maqindel_ret_destroy( bam_maqindel_ret_t * )
+
+#  bam_maqindel_opt_t *bam_maqindel_opt_init()
+
+#  bam_maqindel_ret_t * bam_maqindel(int n, 
+#  		     int pos, 
+#  		     bam_maqindel_opt_t * mi, 
+#  		     bam_pileup1_t * pl, 
+#		     char *ref,
+#		     int _n_types, 
+#		     int * _types )
+                                                               
+
 cdef extern from "faidx.h":
 
    ctypedef struct faidx_t:
@@ -256,6 +346,7 @@ cdef extern from "faidx.h":
    char *faidx_fetch_seq(faidx_t *fai, char *c_name, 
                          int p_beg_i, int p_end_i, int *len)
 
+
 cdef extern from "pysam_util.h":
 
     int pysam_pileup_next(bam1_t *b, 
@@ -280,4 +371,66 @@ cdef extern from "pysam_util.h":
     # translate char to unsigned char
     unsigned char pysam_translate_sequence( char s )
 
-    
+    unsigned char * bam_nt16_table
+
+    int pysam_reference2tid( bam_header_t *header, char * s )
+
+    void pysam_set_stderr( FILE * file )
+
+    # return mapped/unmapped reads on tid
+    uint32_t pysam_get_mapped( bam_index_t *idx, int tid )
+    uint32_t pysam_get_unmapped( bam_index_t *idx, int tid )
+
+#    uint32_t pysam_glf_depth( glf1_t * g )
+
+#    void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c )
+
+# need to declare all C fields and methods here
+cdef class AlignedRead:
+
+    # object that this AlignedRead represents
+    cdef bam1_t * _delegate
+
+cdef class Samfile:
+    cdef char * _filename
+    # pointer to samfile
+    cdef samfile_t * samfile
+    # pointer to index
+    cdef bam_index_t *index
+    # true if file is a bam file
+    cdef int isbam
+    # true if not a file but a stream
+    cdef int isstream
+    # true if file is not on the local filesystem
+    cdef int isremote
+    # current read within iteration
+    cdef bam1_t * b
+    # file opening mode
+    cdef char * mode
+
+    # beginning of read section
+    cdef int64_t start_offset 
+
+    cdef bam_header_t * _buildHeader( self, new_header )
+    cdef bam1_t * getCurrent( self )
+    cdef int cnext(self)
+
+    # write an aligned read
+    cpdef int write( self, AlignedRead read )
+
+    cdef char * _getrname( self, int tid )
+
+cdef class IteratorRow:
+    pass
+
+cdef class IteratorRowAll(IteratorRow):
+    cdef bam1_t * b
+    cdef samfile_t * fp
+    # true if samfile belongs to this object
+    cdef int owns_samfile
+
+    cdef bam1_t * getCurrent( self )
+
+    cdef int cnext(self)
+
+