From 64e353ce49dabca10789b940d260b381293cf528 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Mon, 28 Nov 2011 09:12:21 -0500
Subject: [PATCH] bugfix: bwa-sw PE segfault in rare case

---
 NEWS          | 33 +++++++++++++++++++++++++++++++++
 bwape.c       |  6 +++---
 bwtsw2_pair.c |  1 +
 3 files changed, 37 insertions(+), 3 deletions(-)

diff --git a/NEWS b/NEWS
index 34d7151..69f27e0 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,36 @@
+Release 0.6.1 (25 November, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes to BWA-short:
+
+ * Bugfix: duplicated alternative hits in the XA tag.
+
+ * Bugfix: when trimming enabled, bwa-aln trims 1bp less.
+
+ * Disabled the color-space alignment. 0.6.x is not working with SOLiD reads at
+   present.
+
+Notable changes to BWA-SW:
+
+ * Bugfix: segfault due to excessive ambiguous bases.
+
+ * Bugfix: incorrect mate position in the SE mode.
+
+ * When macro _NO_SSE2 is in use, fall back to the standard Smith-Waterman
+   instead of SSE2-SW.
+
+ * Optionally mark split hits with lower alignment scores as secondary.
+
+Changes to fastmap:
+
+ * Bugfix: infinite loop caused by ambiguous bases.
+
+ * Optionally output the query sequence.
+
+(0.6.1: 25 November 2011, r103)
+
+
+
 Release 0.5.10 and 0.6.0 (12 November, 2011)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
diff --git a/bwape.c b/bwape.c
index 204bbfe..e2c4c96 100644
--- a/bwape.c
+++ b/bwape.c
@@ -437,7 +437,7 @@ bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const u
 	bwa_cigar_t *cigar = 0;
 	ubyte_t *ref_seq;
 	bwtint_t k, x, y, l;
-	int path_len, ret;
+	int path_len, ret, subo;
 	AlnParam ap = aln_param_bwa;
 	path_t *path, *p;
 
@@ -454,8 +454,8 @@ bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const u
 	path = (path_t*)calloc(l+len, sizeof(path_t));
 
 	// do alignment
-	ret = aln_local_core(ref_seq, l, (ubyte_t*)seq, len, &ap, path, &path_len, 1, 0);
-	if (ret < 0) {
+	ret = aln_local_core(ref_seq, l, (ubyte_t*)seq, len, &ap, path, &path_len, 1, &subo);
+	if (ret < 0 || subo == ret) { // no hit or tandem hits
 		free(path); free(cigar); free(ref_seq); *n_cigar = 0;
 		return 0;
 	}
diff --git a/bwtsw2_pair.c b/bwtsw2_pair.c
index ad1bb3f..5e1ec7c 100644
--- a/bwtsw2_pair.c
+++ b/bwtsw2_pair.c
@@ -111,6 +111,7 @@ void bsw2_pair1(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, const b
 	}
 	if (beg < 1) beg = 1;
 	if (end > l_pac) end = l_pac;
+	if (end - beg < l_mseq) return;
 	// generate the sequence
 	seq = malloc(l_mseq + (end - beg));
 	ref = seq + l_mseq;