From 6e3fa0515ad8a8374f33fbab432f4133011554cc Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 20 Nov 2013 09:50:46 -0500
Subject: [PATCH] r420: inferred bandwidth is not used in the final

---
 bwamem.c | 4 +++-
 main.c   | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/bwamem.c b/bwamem.c
index c1f190f..689c74e 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -920,7 +920,9 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
 		exit(1);
 	}
 	w2 = infer_bw(qe - qb, re - rb, ar->truesc, opt->a, opt->q, opt->r);
-	w2 = w2 < opt->w? w2 : opt->w;
+	if (bwa_verbose >= 4) fprintf(stderr, "Band width: infer=%d, opt=%d, alnreg=%d\n", w2, opt->w, ar->w);
+	if (w2 > opt->w) w2 = w2 < ar->w? w2 : ar->w;
+	else w2 = opt->w;
 	a.cigar = bwa_gen_cigar(opt->mat, opt->q, opt->r, w2, bns->l_pac, pac, qe - qb, (uint8_t*)&query[qb], rb, re, &score, &a.n_cigar, &NM);
 	a.NM = NM;
 	pos = bns_depos(bns, rb < bns->l_pac? rb : re - 1, &is_rev);
diff --git a/main.c b/main.c
index a783924..fb90dbd 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.5a-r419"
+#define PACKAGE_VERSION "0.7.5a-r420"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);