[Bio-bwa-help] BWASW bug

[Nils H. <nil...@gm...>]

Below you will find a quick diff that fixes a bug in "bwa bwasw".  This
causes a segmentation fault in extreme case.

Sincerely,

Nils Homer

svn diff
Index: bwtsw2_aux.c
===================================================================
--- bwtsw2_aux.c    (revision 50)
+++ bwtsw2_aux.c    (working copy)
@@ -290,7 +290,7 @@
     for (i = 0; i < b[0]->n; ++i) {
         bsw2hit_t *p = b[0]->hits + i;
         for (j = 0; j < b[1]->n; ++j) {
-            bsw2hit_t *q = b[1]->hits + i;
+            bsw2hit_t *q = b[1]->hits + j;
             if (q->beg == p->beg && q->end == p->end && q->k == p->k &&
q->len == p->len && q->G == p->G) {
                 q->flag |= 0x30000; p->flag |= 0x30000;
                 break;