40c81e91db52a631be33daca5c8ecdccb5213f64
ceisenhart
  Sat May 24 23:30:48 2014 -0700
Removed test functions and white space, camel cased variables and added comments.
diff --git src/utils/bamSplitByChrom/bamSplitByChrom.c src/utils/bamSplitByChrom/bamSplitByChrom.c
index e20a4e8..612148f 100644
--- src/utils/bamSplitByChrom/bamSplitByChrom.c
+++ src/utils/bamSplitByChrom/bamSplitByChrom.c
@@ -1,89 +1,76 @@
 /* bamSplitByChrom -  Splits a bam file into multiple bam files based on chromosome . */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "bamFile.h"
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bamSplitByChrom -  Splits a bam file into multiple bam files based on chromosome \n"
   "usage:\n"
   "   bamSplitByChrom input.bam\n"
   "options:\n"
-  "   -prefix= chromosome prefix\n"
+  "   \n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 void printBamSeq()
 {
 }
 
 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 chroms(bam_header_t *head, bam1_t one, FILE *f, samfile_t *in)
-
-{
-int z;
-
-    for (z=0; z<head->n_targets; ++z)
-        {
-        fprintf(f, "%s\n",head->target_name[z]);
-        }
-    
-}
 void bamSplitByChrom(char *inBam)
 /* bamSplitByChrom -  Splits a bam file into multiple bam files based on chromosome . */
 {
 /* Open file and get header for it. */
 samfile_t *in = samMustOpen(inBam, "rb", NULL);
 bam_header_t *head = in->header;
 bam1_t one;
-FILE *f = mustOpen("chroms", "w");
 ZeroVar(&one);	// This seems to be necessary!
-chroms(head,one,f,in);
 int i =0;
 for (i=0; i<head->n_targets; ++i)
+/* Loop through each chromosome. */   
    { 
-   
     char *outBam = head->target_name[i];  
     samfile_t *out = bamMustOpenLocal(outBam, "wb", head);
+    /* Open an output bam file. */
     for (;;)
+    /* Loop through the input bam file. */
         {
         if (samread(in, &one) < 0)
             {
 	    break;
 	    }
 	if (head->target_name[one.core.tid]==outBam)
 	    {
             samwrite(out, &one);
             }
         }
-
     samclose(out);
     }
-
 samclose(in);   
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 2)
     usage();
 bamSplitByChrom(argv[1]);
 return 0;
 }