From 3bd33508d7e046c7256684c2ada0fe5644ac98ae Mon Sep 17 00:00:00 2001 From: peterjc Date: Wed, 16 Nov 2011 10:04:16 +0000 Subject: [PATCH] bam_calend should count CIGAR X/= operators --- bam.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bam.c b/bam.c index 0055e84..71132d3 100644 --- a/bam.c +++ b/bam.c @@ -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;