From 099c24f5fcef8c22f3f2f60603da7963d56ca24a Mon Sep 17 00:00:00 2001
From: Steven Leonard <srl@sanger.ac.uk>
Date: Thu, 11 Feb 2016 14:00:18 +0000
Subject: [PATCH] fix assertion failure report on bio-bwa-help mailing list
 bwase.c:180: bwa_refine_gapped_core: Assertion `re - rb == rlen' failed

---
 bwape.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bwape.c b/bwape.c
index a5dc3ad..f2d3d8e 100644
--- a/bwape.c
+++ b/bwape.c
@@ -379,7 +379,7 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
 						bwt_multi1_t *q = p[j]->multi + k;
 						q->pos = bwa_sa2pos(bns, bwt, q->pos, p[j]->len + q->ref_shift, &strand);
 						q->strand = strand;
-						if (q->pos != p[j]->pos)
+						if (q->pos != p[j]->pos && q->pos != (bwtint_t)-1)
 							p[j]->multi[n_multi++] = *q;
 					}
 					p[j]->n_multi = n_multi;