X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=pysam%2Fcsamtools.pxd;h=df3763802d7ee5742a5379acbfc43b4d052ddf6d;hp=7dac38d2d887b5e24e8244df4287d2d1b518ed7c;hb=e1756c41e7a1d7cc01fb95e42df9dd04da2d2991;hpb=aa8ecff068edbb09a03bd874fce716e93e22e53c

diff --git a/pysam/csamtools.pxd b/pysam/csamtools.pxd
index 7dac38d..df37638 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
@@ -27,7 +29,7 @@ cdef extern from "stdio.h":
   FILE * stdout
   int fclose(FILE *)
   int sscanf(char *str,char *fmt,...)
-  int printf(char *str,char *fmt,...)
+  int printf(char *fmt,...)
   int sprintf(char *str,char *fmt,...)
   int fprintf(FILE *ifile,char *fmt,...)
   char *fgets(char *str,int size,FILE *ifile)
@@ -50,6 +52,14 @@ cdef extern from "string.h":
   size_t strlen(char *s)
   int memcmp( void * s1, void *s2, size_t len )
 
+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
 
@@ -60,9 +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
 
@@ -120,15 +131,45 @@ cdef extern from "bam.h":
   ctypedef struct bam_plbuf_t:
       pass
 
+  ctypedef struct pair64_t:
+      uint64_t u, v
+      
+  ctypedef struct bam_iter_t:
+      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 *)
+
   bamFile razf_dopen(int data_fd, char *mode)
 
-  # removed - macros not found
+  int64_t bam_seek( bamFile fp, uint64_t voffset, int where)
+  int64_t bam_tell( bamFile fp )
 
-  # int64_t bam_seek( bamFile fp, uint64_t voffset, int where)
-  # int64_t bam_tell( bamFile fp )
-  # void bam_destroy1( bam1_t * b) 
   # void bam_init_header_hash(bam_header_t *header)
 
+  ###############################################
+  # stand-ins for samtools macros
+  uint32_t * bam1_cigar( bam1_t * b)
+  char * bam1_qname( bam1_t * b)
+  uint8_t * bam1_seq( bam1_t * b)
+  uint8_t * bam1_qual( bam1_t * b)
+  uint8_t * bam1_aux( bam1_t * b)
+
+  ###############################################
+  # bam iterator interface
+  bam_iter_t bam_iter_query( bam_index_t *idx, int tid, int beg, int end)
+
+  int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b)
+
+  void bam_iter_destroy(bam_iter_t iter)
+
+  ###############################################
+
   bam1_t * bam_dup1( bam1_t *src ) 
   
   bam1_t * bam_copy1(bam1_t *bdst, bam1_t *bsrc)
@@ -138,6 +179,7 @@ cdef extern from "bam.h":
 
   int bam_parse_region(bam_header_t *header, char *str, int *ref_id, int *begin, int *end)
 
+  ###############################################
   bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
 
   int bam_fetch(bamFile fp, bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
@@ -145,9 +187,27 @@ cdef extern from "bam.h":
   int bam_plbuf_push(bam1_t *b, bam_plbuf_t *buf)
 
   void bam_plbuf_destroy(bam_plbuf_t *buf)
+  ########################################
+  # pileup iterator interface
+  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)
+  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)
 
-  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()
@@ -164,7 +224,7 @@ 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)
@@ -174,6 +234,9 @@ 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:
@@ -186,7 +249,7 @@ 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)
 
@@ -196,6 +259,73 @@ 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:
@@ -209,15 +339,21 @@ cdef extern from "faidx.h":
 
    char *fai_fetch(faidx_t *fai, char *reg, int *len)
 
-cdef extern from "pysam_util.h":
+   int faidx_fetch_nseq(faidx_t *fai)
 
-    int pysam_bam_plbuf_push(bam1_t *b, bam_plbuf_t *buf, int cont)
+   char *faidx_fetch_seq(faidx_t *fai, char *c_name, 
+                         int p_beg_i, int p_end_i, int *len)
 
-    int pysam_get_pos( bam_plbuf_t *buf)
 
-    int pysam_get_tid( bam_plbuf_t *buf)
+cdef extern from "pysam_util.h":
+
+    int pysam_pileup_next(bam1_t *b, 
+                          bam_plbuf_t *buf, 
+                          bam_pileup1_t ** plp,
+                          int * tid,
+                          int * pos,
+                          int * n_plp )
 
-    bam_pileup1_t * pysam_get_pileup( bam_plbuf_t *buf)
 
     int pysam_dispatch(int argc, char *argv[] )
 
@@ -233,19 +369,43 @@ cdef extern from "pysam_util.h":
     # translate char to unsigned char
     unsigned char pysam_translate_sequence( char s )
 
-    # stand-ins for samtools macros
-    uint32_t * pysam_bam1_cigar( bam1_t * b)
-    char * pysam_bam1_qname( bam1_t * b)
-    uint8_t * pysam_bam1_seq( bam1_t * b)
-    uint8_t * pysam_bam1_qual( bam1_t * b)
-    uint8_t * pysam_bam1_aux( bam1_t * b)
+    unsigned char * bam_nt16_table
+
+    int pysam_reference2tid( bam_header_t *header, char * s )
+
+    void pysam_set_stderr( FILE * file )
+
+    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 file is not on the local filesystem
+    cdef int isremote
+    # current read within iteration
+    cdef bam1_t * b
+    # file opening mode
+    cdef char * mode
+
+    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 )
 
-    # iterator implemenation
-    ctypedef struct bam_fetch_iterator_t:
-        pass
-  
-    bam_fetch_iterator_t* bam_init_fetch_iterator(bamFile fp, bam_index_t *idx, int tid, int beg, int end)
-  
-    bam1_t * bam_fetch_iterate(bam_fetch_iterator_t *iter)
-  
-    void bam_cleanup_fetch_iterator(bam_fetch_iterator_t *iter)