int bam_fillmd(int argc, char *argv[])
{
- int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0, is_realn, is_capQ;
+ int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0, is_realn, capQ = 0;
samfile_t *fp, *fpout = 0;
faidx_t *fai;
char *ref = 0, mode_w[8], mode_r[8];
bam1_t *b;
- is_bam_out = is_sam_in = is_uncompressed = is_realn = is_capQ = 0;
+ is_bam_out = is_sam_in = is_uncompressed = is_realn = 0;
mode_w[0] = mode_r[0] = 0;
strcpy(mode_r, "r"); strcpy(mode_w, "w");
- while ((c = getopt(argc, argv, "reubSCn:")) >= 0) {
+ while ((c = getopt(argc, argv, "reubSC:n:")) >= 0) {
switch (c) {
case 'r': is_realn = 1; break;
case 'e': is_equal = 1; break;
case 'u': is_uncompressed = is_bam_out = 1; break;
case 'S': is_sam_in = 1; break;
case 'n': max_nm = atoi(optarg); break;
- case 'C': is_capQ = 1; break;
+ case 'C': capQ = atoi(optarg); break;
default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
}
}
fp->header->target_name[tid]);
}
if (is_realn) bam_realn(b, ref);
- if (is_capQ) {
- int q = bam_cap_mapQ(b, ref, 40);
+ if (capQ > 10) {
+ int q = bam_cap_mapQ(b, ref, capQ);
if (b->core.qual > q) b->core.qual = q;
}
if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm);