From d33abf127f2f5cbe4a3129d10b8f85a501a21857 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 29 Mar 2012 14:45:00 -0400
Subject: [PATCH] check *.64.bwt first and then *.bwt

---
 bwtaln.c | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/bwtaln.c b/bwtaln.c
index 9db63c8..014734c 100644
--- a/bwtaln.c
+++ b/bwtaln.c
@@ -227,17 +227,19 @@ char *bwa_infer_prefix(const char *hint)
 	l_hint = strlen(hint);
 	prefix = malloc(l_hint + 3 + 4 + 1);
 	strcpy(prefix, hint);
-	strcpy(prefix + l_hint, ".bwt");
+	strcpy(prefix + l_hint, ".64.bwt");
 	if ((fp = fopen(prefix, "rb")) != 0) {
-		prefix[l_hint] = 0;
+		fclose(fp);
+		prefix[l_hint + 3] = 0;
 		return prefix;
 	} else {
-		strcpy(prefix + l_hint, ".64.bwt");
+		strcpy(prefix + l_hint, ".bwt");
 		if ((fp = fopen(prefix, "rb")) == 0) {
 			free(prefix);
 			return 0;
 		} else {
-			prefix[l_hint + 3] = 0;
+			fclose(fp);
+			prefix[l_hint] = 0;
 			return prefix;
 		}
 	}