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bam_calend should count CIGAR X/= operators #6

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bam_calend should count CIGAR X/= operators #6

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2 changes: 1 addition & 1 deletion bam.c
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
end = c->pos;
for (k = 0; k < c->n_cigar; ++k) {
int op = cigar[k] & BAM_CIGAR_MASK;
if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL || op == BAM_CREF_SKIP)
end += cigar[k] >> BAM_CIGAR_SHIFT;
}
return end;
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