From 8437cd4edde26eff4c48bc77e0ec15ca9b535dd8 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 19 Mar 2013 01:04:57 -0400
Subject: [PATCH] r369: bugfix - segfault caused by the last change

Sigh... Even the simplest change can lead to new bugs.
---
 bwamem.c | 51 ++++++++++++++++++++++++++-------------------------
 main.c   |  2 +-
 2 files changed, 27 insertions(+), 26 deletions(-)

diff --git a/bwamem.c b/bwamem.c
index 1af7f87..d19848d 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -759,37 +759,38 @@ int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
 void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m)
 {
 	kstring_t str;
+	kvec_t(mem_aln_t) aa;
+	int k;
+
+	kv_init(aa);
 	str.l = str.m = 0; str.s = 0;
-	if (a->n > 0 && a->a[0].score >= opt->T) {
-		int k;
-		kvec_t(mem_aln_t) aa;
-		kv_init(aa);
-		for (k = 0; k < a->n; ++k) {
-			mem_alnreg_t *p = &a->a[k];
-			mem_aln_t *q;
-			if (p->score < opt->T) continue;
-			if (p->secondary >= 0 && !(opt->flag&MEM_F_ALL)) continue;
-			if (p->secondary >= 0 && p->score < a->a[p->secondary].score * .5) continue;
-			q = kv_pushp(mem_aln_t, aa);
-			*q = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, p);
-			if (q->rid < 0) { // unfixable cross-reference alignment
-				--aa.n;
-				continue;
-			}
-			q->flag |= extra_flag | (p->secondary >= 0? 0x100 : 0); // flag secondary
-			if (p->secondary >= 0) q->sub = -1; // don't output sub-optimal score
-			if ((opt->flag&MEM_F_NO_MULTI) && k && p->secondary < 0) q->flag |= 0x10000;
-			if (k && q->mapq > aa.a[0].mapq) q->mapq = aa.a[0].mapq;
+	for (k = 0; k < a->n; ++k) {
+		mem_alnreg_t *p = &a->a[k];
+		mem_aln_t *q;
+		if (p->score < opt->T) continue;
+		if (p->secondary >= 0 && !(opt->flag&MEM_F_ALL)) continue;
+		if (p->secondary >= 0 && p->score < a->a[p->secondary].score * .5) continue;
+		q = kv_pushp(mem_aln_t, aa);
+		*q = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, p);
+		if (q->rid < 0) { // unfixable cross-reference alignment
+			--aa.n;
+			continue;
 		}
-		for (k = 0; k < aa.n; ++k)
-			mem_aln2sam(bns, &str, s, aa.n, aa.a, k, m);
-		for (k = 0; k < aa.n; ++k) free(aa.a[k].cigar);
-		free(aa.a);
-	} else {
+		q->flag |= extra_flag | (p->secondary >= 0? 0x100 : 0); // flag secondary
+		if (p->secondary >= 0) q->sub = -1; // don't output sub-optimal score
+		if ((opt->flag&MEM_F_NO_MULTI) && k && p->secondary < 0) q->flag |= 0x10000;
+		if (k && q->mapq > aa.a[0].mapq) q->mapq = aa.a[0].mapq;
+	}
+	if (aa.n == 0) { // no alignments good enough; then write an unaligned record
 		mem_aln_t t;
 		t = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, 0);
 		t.flag |= extra_flag;
 		mem_aln2sam(bns, &str, s, 1, &t, 0, m);
+	} else {
+		for (k = 0; k < aa.n; ++k)
+			mem_aln2sam(bns, &str, s, aa.n, aa.a, k, m);
+		for (k = 0; k < aa.n; ++k) free(aa.a[k].cigar);
+		free(aa.a);
 	}
 	s->sam = str.s;
 }
diff --git a/main.c b/main.c
index 0a79581..54c3093 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.3-r368-beta"
+#define PACKAGE_VERSION "0.7.3-r369-beta"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);