df2fa6d28c556dd7d12b5bbb9ff06406aaa132f0
ceisenhart
  Fri May 30 22:23:26 2014 -0700
Removed a function that was librarified, updated comments and stylistic errors
diff --git src/utils/bamMerge/bamMerge.c src/utils/bamMerge/bamMerge.c
index 622bc7c..6a25028 100644
--- src/utils/bamMerge/bamMerge.c
+++ src/utils/bamMerge/bamMerge.c
@@ -11,53 +11,44 @@
 {
 errAbort(
   "bamMerge -  Merges multiple bam files into a single bam file \n"
   "usage:\n"
   "   bamMerge input1.bam input2.bam ... inputn.bam\n"
   "options:\n"
   "   \n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
-samfile_t *samMustOpen(char *fileName, char *mode, void *extraHeader)
-/* Open up samfile or die trying. */
-{
-samfile_t *sf = samopen(fileName, mode, extraHeader);
-if (sf == NULL)
-    errnoAbort("Couldn't open %s.\n", fileName);
-return sf;
-}
 
 void bamMerge(char *fileNames[], int files)
 /* bamMerge -  Merges multiple bam files into a single bam file. */
 {
-samfile_t *chromHead =samMustOpen(fileNames[1], "rb", NULL);
-char *outBam = "merged.bam";
+samfile_t *chromHead = bamMustOpenLocal(fileNames[1], "rb", NULL);
 bam_header_t *head = chromHead->header;
-samfile_t *out = bamMustOpenLocal(outBam, "wb", head);
+samfile_t *out = bamMustOpenLocal("merged.bam", "wb", head);
 samclose(chromHead);
 /* Opens the output and sets the header to be the same as the first input. */
 int i;
 for (i = 1; i < files; ++i)
 /* Loop through all input files */
     {
-    samfile_t *in = samMustOpen(fileNames[i], "rb", NULL);
+    samfile_t *in = bamMustOpenLocal(fileNames[i], "rb", NULL);
     bam1_t one;
     ZeroVar(&one);	// This seems to be necessary!
     /* Open an input file */
     for (;;)
         {
         if (samread(in, &one) < 0)
             {
 	    break;
 	    }
         samwrite(out, &one);
         /* Copy the input to the output */
 	}
     samclose(in);
     }
 samclose(out);