-// stand-ins for samtools macros in bam.h
-char * pysam_bam1_qname( const bam1_t * b)
-{
- return (char*)b->data;
-}
-
-uint32_t * pysam_bam1_cigar( const bam1_t * b)
-{
- return (uint32_t*)(b->data + b->core.l_qname);
-}
-
-uint8_t * pysam_bam1_seq( const bam1_t * b)
-{
- return (uint8_t*)(b->data + b->core.n_cigar*4 + b->core.l_qname);
-}
-
-uint8_t * pysam_bam1_qual( const bam1_t * b)
-{
- return (uint8_t*)(b->data + b->core.n_cigar*4 + b->core.l_qname + (b->core.l_qseq + 1)/2);
-}
-
-uint8_t * pysam_bam1_aux( const bam1_t * b)
-{
- return (uint8_t*)(b->data + b->core.n_cigar*4 + b->core.l_qname + b->core.l_qseq + (b->core.l_qseq + 1)/2);
-}
-
-// #######################################################
-// Iterator implementation
-// #######################################################
-
-// functions defined in bam_index.c
-extern pair64_t * get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int* cnt_off);
-
-static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
-{
- uint32_t rbeg = b->core.pos;
- uint32_t rend = b->core.n_cigar? bam_calend(&b->core, bam1_cigar(b)) : b->core.pos + 1;
- return (rend > beg && rbeg < end);
-}
-
-struct __bam_fetch_iterator_t
-{
- bam1_t * b;
- pair64_t * off;
- int n_off;
- uint64_t curr_off;
- int curr_chunk;
- bamFile fp;
- int tid;
- int beg;
- int end;
- int n_seeks;
-};
-
-bam_fetch_iterator_t* bam_init_fetch_iterator(bamFile fp, const bam_index_t *idx, int tid, int beg, int end)
-{
- // iterator contains current alignment position
- // and will contain actual alignment during iterations
- bam_fetch_iterator_t* iter = (bam_fetch_iterator_t*)calloc(1, sizeof(bam_fetch_iterator_t));
- iter->b = (bam1_t*)calloc(1, sizeof(bam1_t));
-
- // list of chunks containing our alignments
- iter->off = get_chunk_coordinates(idx, tid, beg, end, &iter->n_off);
-
- // initialise other state variables in iterator
- iter->fp = fp;
- iter->curr_chunk = -1;
- iter->curr_off = 0;
- iter->n_seeks = 0;
- iter->tid = tid;
- iter->beg = beg;
- iter->end = end;
- return iter;
-}
-
-bam1_t * bam_fetch_iterate(bam_fetch_iterator_t *iter)
-{
- if (!iter->off) {
- return 0;
- }
-
- int ret;
- // iterate through all alignments in chunks
- for (;;) {
- if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->curr_chunk].v) { // then jump to the next chunk
- if (iter->curr_chunk == iter->n_off - 1) break; // no more chunks
- if (iter->curr_chunk >= 0) assert(iter->curr_off == iter->off[iter->curr_chunk].v); // otherwise bug
- if (iter->curr_chunk < 0 || iter->off[iter->curr_chunk].v != iter->off[iter->curr_chunk+1].u) { // not adjacent chunks; then seek
- bam_seek(iter->fp, iter->off[iter->curr_chunk+1].u, SEEK_SET);
- iter->curr_off = bam_tell(iter->fp);
- ++iter->n_seeks;
- }
- ++iter->curr_chunk;
- }
- if ((ret = bam_read1(iter->fp, iter->b)) > 0) {
- iter->curr_off = bam_tell(iter->fp);
- if (iter->b->core.tid != iter->tid || iter->b->core.pos >= iter->end) break; // no need to proceed
- else if (is_overlap(iter->beg, iter->end, iter->b))
- //
- //func(iter->b, data);
- //
- return iter->b;
- } else
- return 0; // end of file
- }
- return 0;
-}
-
-void bam_cleanup_fetch_iterator(bam_fetch_iterator_t *iter)
-{
- // fprintf(stderr, "[bam_fetch] # seek calls: %d\n", iter->n_seeks);
- bam_destroy1(iter->b);
- free(iter->off);
-}