From: On behalf of John Marshall <lh3@sanger.ac.uk>
Date: Mon, 30 Nov 2009 12:09:04 +0000 (+0000)
Subject: Index files should be opened in binary mode, not text mode.
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;ds=sidebyside;h=185ac166fd66907c8435f4d371582c972695bd4c;p=samtools.git

Index files should be opened in binary mode, not text mode.
---

diff --git a/bam_index.c b/bam_index.c
index a627884..853ac70 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -339,13 +339,13 @@ bam_index_t *bam_index_load_local(const char *_fn)
 	} else fn = strdup(_fn);
 	fnidx = (char*)calloc(strlen(fn) + 5, 1);
 	strcpy(fnidx, fn); strcat(fnidx, ".bai");
-	fp = fopen(fnidx, "r");
+	fp = fopen(fnidx, "rb");
 	if (fp == 0) { // try "{base}.bai"
 		char *s = strstr(fn, "bam");
 		if (s == fn + strlen(fn) - 3) {
 			strcpy(fnidx, fn);
 			fnidx[strlen(fn)-1] = 'i';
-			fp = fopen(fnidx, "r");
+			fp = fopen(fnidx, "rb");
 		}
 	}
 	free(fnidx); free(fn);
@@ -375,7 +375,7 @@ static void download_from_remote(const char *url)
 		fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
 		return;
 	}
-	if ((fp = fopen(fn, "w")) == 0) {
+	if ((fp = fopen(fn, "wb")) == 0) {
 		fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
 		knet_close(fp_remote);
 		return;
@@ -425,7 +425,7 @@ int bam_index_build2(const char *fn, const char *_fnidx)
 		fnidx = (char*)calloc(strlen(fn) + 5, 1);
 		strcpy(fnidx, fn); strcat(fnidx, ".bai");
 	} else fnidx = strdup(_fnidx);
-	fpidx = fopen(fnidx, "w");
+	fpidx = fopen(fnidx, "wb");
 	if (fpidx == 0) {
 		fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
 		free(fnidx);