khash_t(64) *hash;
uint32_t format;
int tid, len, last_pos;
- int mask;
+ int mask, min_mapQ;
char *ref;
glfFile fp_glf; // for glf output only
} pu_data_t;
d->tid = -1; d->mask = BAM_DEF_MASK;
d->c = bam_maqcns_init();
d->ido = bam_maqindel_opt_init();
- while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:")) >= 0) {
+ while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:q:")) >= 0) {
switch (c) {
case 's': d->format |= BAM_PLF_SIMPLE; break;
case 't': fn_list = strdup(optarg); break;
case 'g': d->format |= BAM_PLF_GLF; break;
case 'I': d->ido->q_indel = atoi(optarg); break;
case 'G': d->ido->r_indel = atof(optarg); break;
+ case 'q': d->min_mapQ = atoi(optarg); break;
default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1;
}
}
fprintf(stderr, "Option: -s simple (yet incomplete) pileup format\n");
fprintf(stderr, " -i only show lines/consensus with indels\n");
fprintf(stderr, " -m INT filtering reads with bits in INT [%d]\n", d->mask);
+ fprintf(stderr, " -q INT filtering reads with mapping quality smaller than INT [%d]\n", d->min_mapQ);
fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", d->c->cap_mapQ);
fprintf(stderr, " -t FILE list of reference sequences (assume the input is in SAM)\n");
fprintf(stderr, " -l FILE list of sites at which pileup is output\n");
}
d->h = fp->header;
if (fn_pos) d->hash = load_pos(fn_pos, d->h);
- sampileup(fp, d->mask, pileup_func, d);
+ sampileup(fp, d->mask, d->min_mapQ, pileup_func, d);
samclose(fp); // d->h will be destroyed here
}