20c459c45647bd0b8bf30cf68da82eafb5f0e5c5
ceisenhart
  Mon Jun 23 18:35:34 2014 -0700
Updated the main for loop to be 0 based index rather than 1 based index
diff --git src/utils/bamMerge/bamMerge.c src/utils/bamMerge/bamMerge.c
index 6a25028..85885be 100644
--- src/utils/bamMerge/bamMerge.c
+++ src/utils/bamMerge/bamMerge.c
@@ -15,53 +15,53 @@
   "   bamMerge input1.bam input2.bam ... inputn.bam\n"
   "options:\n"
   "   \n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 
 void bamMerge(char *fileNames[], int files)
 /* bamMerge -  Merges multiple bam files into a single bam file. */
 {
-samfile_t *chromHead = bamMustOpenLocal(fileNames[1], "rb", NULL);
+samfile_t *chromHead = bamMustOpenLocal(fileNames[0], "rb", NULL);
 bam_header_t *head = chromHead->header;
 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)
+for (i = 0; i < files - 1; ++i)
 /* Loop through all input files */
     {
     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);
 }
 
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc < 2)
     usage();   
-bamMerge(argv,argc);
+bamMerge(argv+1,argc);
 return 0;
 
 }