Merge commit 'upstream/0.3'

[pysam.git] / pysam / csamtools.pxd

diff --git a/pysam/csamtools.pxd b/pysam/csamtools.pxd
index 7dac38d2d887b5e24e8244df4287d2d1b518ed7c..b614a844fa8cb9d75ef33cdef7a11a6c81d2e1ad 100644 (file)
--- a/pysam/csamtools.pxd
+++ b/pysam/csamtools.pxd
@@ -27,7 +27,7 @@ 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 +50,9 @@ 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*)
+
 cdef extern from "razf.h":
   pass
 
@@ -120,15 +123,37 @@ cdef extern from "bam.h":
   ctypedef struct bam_plbuf_t:
       pass
 
+  ctypedef struct bam_iter_t:
+      pass
+
+  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 +163,7 @@ 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)
@@ -145,6 +171,22 @@ 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 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)
 
@@ -209,15 +251,20 @@ 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)
+cdef extern from "pysam_util.h":
 
-    int pysam_get_tid( bam_plbuf_t *buf)
+    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 +280,4 @@ 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)
-
-    # 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)
+