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New upstream release.
[samtools.git]
/
bam.c
diff --git
a/bam.c
b/bam.c
index 5fac17df6ec27d7cbb04b5600c3ce54d5c06b354..0055e8427667dd95151ea1a1bef5dd14e74e15f1 100644
(file)
--- a/
bam.c
+++ b/
bam.c
@@
-32,7
+32,7
@@
int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
int32_t l = 0;
for (k = 0; k < c->n_cigar; ++k) {
int op = cigar[k] & BAM_CIGAR_MASK;
int32_t l = 0;
for (k = 0; k < c->n_cigar; ++k) {
int op = cigar[k] & BAM_CIGAR_MASK;
- if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP)
+ if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP
|| op == BAM_CEQUAL || op == BAM_CDIFF
)
l += cigar[k] >> BAM_CIGAR_SHIFT;
}
return l;
l += cigar[k] >> BAM_CIGAR_SHIFT;
}
return l;
@@
-268,7
+268,7
@@
char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
else {
for (i = 0; i < c->n_cigar; ++i) {
kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
else {
for (i = 0; i < c->n_cigar; ++i) {
kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
- kputc("MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
+ kputc("MIDNSHP
=X
"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
}
}
kputc('\t', &str);
}
}
kputc('\t', &str);