From e2cd2d71f7db8816b074c1561b72970d0c9e493d Mon Sep 17 00:00:00 2001
From: Henry Amrhein <hamrhein@caltech.edu>
Date: Wed, 2 Jan 2013 12:58:36 -0800
Subject: [PATCH] bam_cat.c: 	check return value of malloc() in bam_cat()

	wrapped fwrite() calls with error-checking
---
 bam_cat.c | 29 +++++++++++++++++++++++------
 1 file changed, 23 insertions(+), 6 deletions(-)

diff --git a/bam_cat.c b/bam_cat.c
index 0fde045..43df917 100644
--- a/bam_cat.c
+++ b/bam_cat.c
@@ -86,7 +86,10 @@ int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam
     }
     if (h) bam_header_write(fp, h);
     
-    buf = (uint8_t*) malloc(BUF_SIZE);
+    if ((buf = (uint8_t*) malloc(BUF_SIZE)) == NULL) {
+        fprintf(stderr, "[%s] failed to allocate input buffer.\n", __func__);
+        return -1;
+    }
     for(i = 0; i < nfn; ++i){
         BGZF *in;
         bam_header_t *old;
@@ -121,14 +124,26 @@ int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam
                     fprintf(stderr, "[%s] ERROR: truncated file?: '%s'.\n", __func__, fn[i]);
                     return -1;
                 }
-                fwrite(ebuf, 1, len, fp_file);
+                if (fwrite(ebuf, 1, len, fp_file) < len) {
+                    fprintf(stderr, "[%s] failed to write to output file.\n", __func__);
+                    return -1;
+		}
                 memcpy(ebuf,ebuf+len,diff);
                 memcpy(ebuf+diff,buf,len);
-            } else {
-                if(j!=0) fwrite(ebuf, 1, es, fp_file);
+            }
+            else {
+                if(j!=0) {
+                    if (fwrite(ebuf, 1, es, fp_file) < es) {
+                        fprintf(stderr, "[%s] failed to write to output file.\n", __func__);
+                        return -1;
+                    }
+                }
                 len-= es;
                 memcpy(ebuf,buf+len,es);
-                fwrite(buf, 1, len, fp_file);
+                if (fwrite(buf, 1, len, fp_file) < len) {
+                    fprintf(stderr, "[%s] failed to write to output file.\n", __func__);
+                    return -1;
+                }
             }
             j=1;
         }
@@ -141,7 +156,9 @@ int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam
             if(((gzip1!=GZIPID1) || (gzip2!=GZIPID2)) || (isize!=0)) {
                 fprintf(stderr, "[%s] WARNING: Unexpected block structure in file '%s'.", __func__, fn[i]);
                 fprintf(stderr, " Possible output corruption.\n");
-                fwrite(ebuf, 1, es, fp_file);
+                if (fwrite(ebuf, 1, es, fp_file) < es) {
+                    fprintf(stderr, " Also, failed to write final block.\n");
+                }
             }
         }
         bam_header_destroy(old);
-- 
2.30.2