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updated main loop to not duplicate hash key
[samtools.git]
/
bam_calnh.c
diff --git
a/bam_calnh.c
b/bam_calnh.c
index 13bb9f724f8891ec8946fe61049dc841491922ed..40ce683d7316719e8bc1b4818ee5f0d5f3d0008c 100644
(file)
--- a/
bam_calnh.c
+++ b/
bam_calnh.c
@@
-12,7
+12,6
@@
bam_calnh_core(samfile_t *in, samfile_t *out)
bam1_t *b;
khint_t k;
uint8_t *oldnh;
bam1_t *b;
khint_t k;
uint8_t *oldnh;
- char *qn = NULL;
khash_t(QNH) *qnh;
int ret;
int64_t savepos;
khash_t(QNH) *qnh;
int ret;
int64_t savepos;
@@
-22,7
+21,7
@@
bam_calnh_core(samfile_t *in, samfile_t *out)
if (savepos < 0)
{
if (savepos < 0)
{
- fprintf(stderr, "[
bam_calnh_core] bam_tell failure\n"
);
+ fprintf(stderr, "[
%s] bam_tell failure.\n", __func__
);
return 1;
}
return 1;
}
@@
-31,37
+30,31
@@
bam_calnh_core(samfile_t *in, samfile_t *out)
while (samread(in, b) >= 0)
{
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)
if (ret == 0)
- {
kh_val(qnh, k) += 1;
kh_val(qnh, k) += 1;
- free(qn);
- }
else
kh_val(qnh, k) = 1;
}
else
kh_val(qnh, k) = 1;
}
- if (
(bam_seek(in->x.bam, savepos, SEEK_SET)
) < 0)
+ 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;
}
return 1;
}
-
while (samread(in, b) >= 0)
{
k = kh_get(QNH, qnh, bam1_qname(b));
oldnh = bam_aux_get(b, "NH");
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);
}
samwrite(out, b);
}