From d69cb33b4658985ba53a2d03fd5557da07cd91fe Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Tue, 5 May 2009 14:10:30 +0000
Subject: [PATCH]  * samtools-0.1.3-13 (r260)  * report error for file I/O
 error

---
 bam_plcmd.c |  4 ++--
 bamtk.c     |  2 +-
 bgzf.c      |  8 ++++++--
 sam.c       |  8 ++++++++
 sam_view.c  | 12 +++++++++---
 5 files changed, 26 insertions(+), 8 deletions(-)

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 23e0dd0..7bc422f 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -304,8 +304,8 @@ int bam_pileup(int argc, char *argv[])
 	{
 		samfile_t *fp;
 		fp = fn_list? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);
-		if (fp->header == 0) {
-			fprintf(stderr, "[bam_pileup] fail to read the BAM header. Abort!\n");
+		if (fp == 0 || fp->header == 0) {
+			fprintf(stderr, "[bam_pileup] fail to read the header: non-exisiting file or wrong format.\n");
 			return 1;
 		}
 		d->h = fp->header;
diff --git a/bamtk.c b/bamtk.c
index 2125ee4..a8972f9 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.3-12 (r259)"
+#define PACKAGE_VERSION "0.1.3-13 (r260)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
diff --git a/bgzf.c b/bgzf.c
index 4314c70..1b5cebe 100644
--- a/bgzf.c
+++ b/bgzf.c
@@ -86,7 +86,9 @@ BGZF*
 open_read(int fd)
 {
     FILE* file = fdopen(fd, "r");
-    BGZF* fp = malloc(sizeof(BGZF));
+    BGZF* fp;
+	if (file == 0) return 0;
+	fp = malloc(sizeof(BGZF));
     fp->file_descriptor = fd;
     fp->open_mode = 'r';
     fp->owned_file = 0;
@@ -107,7 +109,9 @@ BGZF*
 open_write(int fd)
 {
     FILE* file = fdopen(fd, "w");
-    BGZF* fp = malloc(sizeof(BGZF));
+    BGZF* fp;
+	if (file == 0) return 0;
+	fp = malloc(sizeof(BGZF));
     fp->file_descriptor = fd;
     fp->open_mode = 'w';
     fp->owned_file = 0;
diff --git a/sam.c b/sam.c
index 8534339..dd6cd3a 100644
--- a/sam.c
+++ b/sam.c
@@ -79,9 +79,11 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 		if (mode[1] == 'b') { // binary
 			fp->type |= TYPE_BAM;
 			fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
+			if (fp->x.bam == 0) goto open_err_ret;
 			fp->header = bam_header_read(fp->x.bam);
 		} else {
 			fp->x.tamr = sam_open(fn);
+			if (fp->x.tamr == 0) goto open_err_ret;
 			fp->header = sam_header_read2(fn_list);
 		}
 	} else if (mode[0] == 'w') {
@@ -89,12 +91,14 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 		if (mode[1] == 'b') { // binary
 			fp->type |= TYPE_BAM;
 			fp->x.bam = strcmp(fn, "-")? bam_open(fn, "w") : bam_dopen(fileno(stdout), "w");
+			if (fp->x.bam == 0) goto open_err_ret;
 			bam_header_write(fp->x.bam, fp->header);
 		} else {
 			int i;
 			bam_header_t *alt = 0;
 			alt = bam_header_parse(fp->header->text);
 			fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
+			if (fp->x.tamr == 0) goto open_err_ret;
 			if (alt) {
 				if (alt->n_targets != fp->header->n_targets)
 					fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
@@ -107,6 +111,10 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 		}
 	}
 	return fp;
+
+open_err_ret:
+	free(fp);
+	return 0;
 }
 
 void samclose(samfile_t *fp)
diff --git a/sam_view.c b/sam_view.c
index 2df0530..cefac2f 100644
--- a/sam_view.c
+++ b/sam_view.c
@@ -21,7 +21,7 @@ static int usage(void);
 int main_samview(int argc, char *argv[])
 {
 	int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0;
-	samfile_t *in, *out;
+	samfile_t *in = 0, *out = 0;
 	char in_mode[4], out_mode[4], *fn_out = 0, *fn_list = 0;
 
 	/* parse command-line options */
@@ -45,8 +45,14 @@ int main_samview(int argc, char *argv[])
 	if (argc == optind) return usage();
 
 	// open file handlers
-	in = samopen(argv[optind], in_mode, fn_list);
-	out = samopen(fn_out? fn_out : "-", out_mode, in->header);
+	if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
+		fprintf(stderr, "[main_samview] fail to open file for reading.\n");
+		goto view_end;
+	}
+	if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
+		fprintf(stderr, "[main_samview] fail to open file for writing.\n");
+		goto view_end;
+	}
 	if (is_header_only) goto view_end; // no need to print alignments
 
 	if (argc == optind + 1) { // convert/print the entire file
-- 
2.39.5