src/utils/bedGraphToBigWig/bedGraphToBigWig.c 1.15

Index: src/utils/bedGraphToBigWig/bedGraphToBigWig.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/bedGraphToBigWig/bedGraphToBigWig.c,v
retrieving revision 1.14
retrieving revision 1.15
diff -b -B -U 4 -r1.14 -r1.15
--- src/utils/bedGraphToBigWig/bedGraphToBigWig.c	12 Aug 2009 21:35:45 -0000	1.14
+++ src/utils/bedGraphToBigWig/bedGraphToBigWig.c	10 Sep 2009 01:49:38 -0000	1.15
@@ -15,9 +15,8 @@
 static char const rcsid[] = "$Id$";
 
 int blockSize = 256;
 int itemsPerSlot = 1024;
-boolean clipDontDie = FALSE;
 
 
 void usage()
 /* Explain usage and exit. */
@@ -32,18 +31,15 @@
   "and out.bw is the output indexed big wig file.\n"
   "options:\n"
   "   -blockSize=N - Number of items to bundle in r-tree.  Default %d\n"
   "   -itemsPerSlot=N - Number of data points bundled at lowest level. Default %d\n"
-  "   -clip - If set just issue warning messages rather than dying if wig\n"
-  "                  file contains items off end of chromosome."
   , blockSize, itemsPerSlot
   );
 }
 
 static struct optionSpec options[] = {
    {"blockSize", OPTION_INT},
    {"itemsPerSlot", OPTION_INT},
-   {"clip", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 struct sectionItem
@@ -249,9 +245,9 @@
     /* Deal with case where might have to split an item between multiple summaries.  This
      * loop handles all but the final affected summary in that case. */
     while (end > sum->end)
         {
-	verbose(2, "Splitting\n");
+	verbose(3, "Splitting start %d, end %d, sum->start %d, sum->end %d\n", start, end, sum->start, sum->end);
 	/* Fold in bits that overlap with existing summary and output. */
 	bits32 overlap = rangeIntersection(start, end, sum->start, sum->end);
 	sum->validCount += overlap;
 	if (sum->minVal > val) sum->minVal = val;
@@ -455,9 +451,8 @@
 {
 optionInit(&argc, argv, options);
 blockSize = optionInt("blockSize", blockSize);
 itemsPerSlot = optionInt("itemsPerSlot", itemsPerSlot);
-clipDontDie = optionExists("clip");
 if (argc != 4)
     usage();
 bedGraphToBigWig(argv[1], argv[2], argv[3]);
 return 0;