コード例 #1
0
ファイル: bam_pileup.c プロジェクト: dtenenba/Rsamtools
int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
{
	int ret, n_plp, tid, pos;
	const bam_pileup1_t *plp;
	ret = bam_plp_push(buf->iter, b);
	if (ret < 0) return ret;
	while ((plp = bam_plp_next(buf->iter, &tid, &pos, &n_plp)) != 0)
		buf->func(tid, pos, n_plp, plp, buf->data);
	return 0;
}
コード例 #2
0
ファイル: bam_pileup.c プロジェクト: dtenenba/Rsamtools
const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
{
	const bam_pileup1_t *plp;
	if (iter->func == 0 || iter->error) { *_n_plp = -1; return 0; }
	if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
	else { // no pileup line can be obtained; read alignments
		*_n_plp = 0;
		if (iter->is_eof) return 0;
		while (iter->func(iter->data, iter->b) >= 0) {
			if (bam_plp_push(iter, iter->b) < 0) {
				*_n_plp = -1;
				return 0;
			}
			if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
			// otherwise no pileup line can be returned; read the next alignment.
		}
		bam_plp_push(iter, 0);
		if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
		return 0;
	}
}
コード例 #3
0
ファイル: bam_access.c プロジェクト: wisekh6/alleleCount
loci_stats *bam_access_get_position_base_counts(char *chr, int posn){
	char *region = NULL;
	hts_itr_t *iter = NULL;
	bam1_t* b = NULL;
	bam_plp_t buf;
	loci_stats *stats = malloc(sizeof(loci_stats *));
	check_mem(stats);
	stats->base_counts = malloc(sizeof(int) * 4);
	check_mem(stats->base_counts);
	stats->base_counts[0] = 0;
	stats->base_counts[1] = 0;
	stats->base_counts[2] = 0;
	stats->base_counts[3] = 0;
	fholder->stats = stats;

	region = malloc((sizeof(char *) * (strlen(chr)+1))+sizeof(":")+sizeof("-")+(sizeof(char)*((no_of_digits(posn)*2)+1)));
	sprintf(region,"%s:%d-%d",chr,posn,posn);
	fholder->beg = posn;
	fholder->end = posn;

  // initialize pileup
	buf = bam_plp_init(pileup_func, (void *)fholder);
	bam_plp_set_maxcnt(buf,maxitercnt);

  /*
  sam_fetch(fholder->in, fholder->idx, ref, fholder->beg, fholder->end, buf, fetch_algo_func);
  */
  //Replace fetch with iterator for htslib compatibility.
  b = bam_init1();
  iter = sam_itr_querys(fholder->idx, fholder->head, region);
  int result;
  int count = 0;
  while ((result = sam_itr_next(fholder->in, iter, b)) >= 0) {
    if(b->core.qual < min_map_qual || (b->core.flag & BAM_FUNMAP)
			|| !(b->core.flag & BAM_FPROPER_PAIR) || (b->core.flag & BAM_FMUNMAP)//Proper pair and mate unmapped
			|| (b->core.flag & BAM_FDUP)//1024 is PCR/optical duplicate
			|| (b->core.flag & BAM_FSECONDARY) || (b->core.flag & BAM_FQCFAIL)//Secondary alignment, quality fail
			|| (b->core.flag & BAM_FSUPPLEMENTARY) ) continue;
    count++;
    bam_plp_push(buf, b);
  }
  sam_itr_destroy(iter);
  bam_plp_push(buf, 0);
  int tid, pos, n_plp = -1;
  const bam_pileup1_t *pil;
  while ( (pil=bam_plp_next(buf, &tid, &pos, &n_plp)) > 0) {
    if((pos+1) != posn) continue;
    int i=0;
   	for(i=0;i<n_plp;i++){
      const bam_pileup1_t *p = pil + i;
      int qual = bam_get_qual(p->b)[p->qpos];
      uint8_t c = bam_seqi(bam_get_seq(p->b), p->qpos);
      if(!(p->is_del) &&  qual >= min_base_qual
            &&  p->b->core.qual >= min_map_qual){
           //&& (c == 1 /*A*/|| c == 2 /*C*/|| c == 4 /*G*/|| c == 8 /*T*/)){
        //Now we add a new read pos struct to the list since the read is valid.
        //char cbase = toupper(bam_nt16_rev_table[c]);
        switch(c){
          case 1:
            fholder->stats->base_counts[0]++;
            break;

          case 2:
            fholder->stats->base_counts[1]++;
            break;

          case 4:
            fholder->stats->base_counts[2]++;
            break;

          case 8:
            fholder->stats->base_counts[3]++;
            break;

          default:
            break;

          }; // End of args switch statement */
   	    }
   	  }
  } //End of iteration through pileup
	//bam_plp_push(buf, 0); // finalize pileup
  bam_plp_destroy(buf);
	free(region);
	return fholder->stats;

error:
	//if(region) free(region);
	if(fholder->stats){
		if(fholder->stats->base_counts) free(fholder->stats->base_counts);
		free(fholder->stats);
	}
	if(iter) sam_itr_destroy(iter);
	if(b) bam_destroy1(b);
	if(region) free(region);
	return NULL;
}