fixed a segfault when there are too few good bases.

dkj · Nov 18, 2011 · 8f89f55 · 8f89f55
1 parent c8edcaf
commit 8f89f55
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Showing 3 changed files with 3 additions and 2 deletions.
diff --git a/bntseq.c b/bntseq.c
@@ -29,6 +29,7 @@
 #include <stdlib.h>
 #include <string.h>
 #include <zlib.h>
+#include <unistd.h>
 #include "bntseq.h"
 #include "main.h"
 #include "utils.h"

diff --git a/bwtsw2_aux.c b/bwtsw2_aux.c
@@ -574,7 +574,7 @@ static void bsw2_aln_core(bsw2seq_t *_seq, const bsw2opt_t *_opt, const bntseq_t
 			rseq[1][i] = c;
 		}
 		if (l - k < opt.t) { // too few unambiguous bases
-			buf[x] = 0;
+			buf[x] = calloc(1, sizeof(bwtsw2_t));
 			free(seq[0]); continue;
 		}
 		// alignment

diff --git a/main.c b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.6.0-r85"
+#define PACKAGE_VERSION "0.6.0-r89-dev"
 #endif
 
 static int usage()