bam1_t *b;
khint_t k;
uint8_t *oldnh;
- char *qn = NULL;
khash_t(QNH) *qnh;
int ret;
int64_t savepos;
if (savepos < 0)
{
- fprintf(stderr, "[bam_calnh_core] bam_tell failure\n");
+ fprintf(stderr, "[%s] bam_tell failure.\n", __func__);
return 1;
}
while (samread(in, b) >= 0)
{
- qn = strdup(bam1_qname(b));
- k = kh_put(QNH, qnh, qn, &ret);
+ k = kh_put(QNH, qnh, bam1_qname(b), &ret);
if (ret == 0)
- {
kh_val(qnh, k) += 1;
- free(qn);
- }
else
kh_val(qnh, k) = 1;
if (bam_seek(in->x.bam, savepos, SEEK_SET) < 0)
{
- fprintf(stderr, "[bam_calnh_core] bam_seek failure\n");
+ fprintf(stderr, "[%s] bam_seek failure.\n", __func__);
return 1;
}
-
while (samread(in, b) >= 0)
{
k = kh_get(QNH, qnh, bam1_qname(b));
oldnh = bam_aux_get(b, "NH");
- if (!(oldnh))
- {
- val = kh_val(qnh, k);
- bam_aux_append(b, "NH", 'i', 4, (uint8_t *)&val);
- }
+ if (oldnh)
+ bam_aux_del(b, oldnh);
+ val = kh_val(qnh, k);
+ bam_aux_append(b, "NH", 'i', 4, (uint8_t *)&val);
samwrite(out, b);
}