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)
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
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)
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)
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)
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[] )
# 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)
+