INNER CODE UNIT · C

seq

dpryan79/MethylDackel · MBias.c:147

        seq = faidx_fetch_seq(fai, hdr->target_name[localTid], localPos, localEnd, &seqlen);
        if(seqlen < 0) {
            fprintf(stderr, "faidx_fetch_seq returned %i while trying to fetch the sequence for tid %s:%"PRIu32"-%"PRIu32"!\n",\
                seqlen, hdr->target_name[localTid], localPos, localEnd);
            fprintf(stderr, "Note that the output will be truncated!\n");
            return NULL;
        }
        data->seq = seq;
        data->lseq = seqlen;
        data->offset = localPos;

        //Start the pileup
        iter = bam_mplp_init(1, filter_func, (void **) &data);
//        bam_mplp_init_overlaps(iter); //This is included in extract but excluded here. The main benefit to exclusion is that you can more accurately gauge overlapping regions.
        bam_mplp_set_maxcnt(iter, INT_MAX);
        while((ret = bam_mplp_auto(iter, &tid, &pos, &n_plp, plp)) > 0) {
            if(pos < localPos || pos >= localEnd) continue; // out of the region requested

View source record →