X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_sort.c;h=03196a8bab9892b5022f477044520c769b2ae557;hb=64fd9dc2c049f72448ff02f5f5c180dfdfe87c60;hp=bbb8f2dbaf0a48b211c789746cec0c3e836371c8;hpb=4c016a8c036a60ae84e7d59d0cb6f49aab35f534;p=samtools.git

diff --git a/bam_sort.c b/bam_sort.c
index bbb8f2d..03196a8 100644
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -321,7 +321,7 @@ static inline int bam1_lt(const bam1_p a, const bam1_p b)
 	if (g_is_by_qname) {
 		int t = strnum_cmp(bam1_qname(a), bam1_qname(b));
 		return (t < 0 || (t == 0 && (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)))));
-	} else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)));
+	} else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)<<1|bam1_strand(a)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)<<1|bam1_strand(b)));
 }
 KSORT_INIT(sort, bam1_p, bam1_lt)