Port #48 to the dev branch

NEWS.md

@@ -1,3 +1,32 @@
+Release 0.7.13 (23 Feburary 2016)
+---------------------------------
+
+This release fixes a few minor bugs in the previous version and adds a few
+minor features. All BWA algorithms should produce identical output to 0.7.12
+when there are no ALT contigs.
+
+Detailed changes:
+
+ * Fixed a bug in "bwa-postalt.js". The old version may produce 0.5% of wrong
+   bases for reads mapped to the ALT contigs.
+
+ * Fixed a potential bug in the multithreading mode. It may occur when mapping
+   is much faster than file reading, which should almost never happen in
+   practice.
+
+ * Changed the download URL of GRCh38.
+
+ * Removed the read overlap mode. It is not working well.
+
+ * Added the ropebwt2 algorithm as an alternative to index large genomes.
+   Ropebwt2 is slower than the "bwtsw" algorithm, but it has a permissive
+   license. This allows us to create an Apache2-licensed BWA (in the "Apache2"
+   branch) for commercial users who are concerned with GPL.
+
+(0.7.13: 23 Feburary 2016, r1118)
+
+
+
 Release 0.7.12 (28 December 2014)
 ---------------------------------
 

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;

bwase.c

@@ -113,6 +113,7 @@ bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int r
 {
 	bwtint_t pos_f;
 	int is_rev;
+	*strand = 0;
 	pos_f = bwt_sa(bwt, sapos); // position on the forward-reverse coordinate
 	if (pos_f < bns->l_pac && bns->l_pac < pos_f + ref_len) return (bwtint_t)-1;
 	pos_f = bns_depos(bns, pos_f, &is_rev); // position on the forward strand; this may be the first base or the last base