* samtools-0.1.2-10

[samtools.git] / bam_index.c

diff --git a/bam_index.c b/bam_index.c
index 59deca071e00824630e076485f643c7bc4c0fa8a..7670c2f3f1058af65086cd40f62f3acbd288025d 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -374,7 +374,7 @@ static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[MAX_BIN])
 static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
 {
        uint32_t rbeg = b->core.pos;
-       uint32_t rend = bam_calend(&b->core, bam1_cigar(b));
+       uint32_t rend = b->core.n_cigar? bam_calend(&b->core, bam1_cigar(b)) : b->core.pos + 1;
        return (rend > beg && rbeg < end);
 }