src/utils/wigToBigWig/wigToBigWig.c 1.6

Index: src/utils/wigToBigWig/wigToBigWig.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/wigToBigWig/wigToBigWig.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/utils/wigToBigWig/wigToBigWig.c	9 Feb 2009 02:53:36 -0000	1.5
+++ src/utils/wigToBigWig/wigToBigWig.c	10 Feb 2009 08:18:18 -0000	1.6
@@ -1,61 +1,61 @@
 /* wigToBigWig - Convert ascii format wig file (in fixedStep, variableStep or bedGraph format) 
  * to binary big wig format.. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "bigWig.h"
 #include "bwgInternal.h"
 
 static char const rcsid[] = "$Id$";
 
 int blockSize = 256;
 int itemsPerSlot = 1024;
 boolean clipDontDie = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "wigToBigWig - Convert ascii format wig file (in fixedStep, variableStep or bedGraph\n"
   "format) to binary big wig format.\n"
   "usage:\n"
   "   wigToBigWig in.wig chrom.sizes out.bw\n"
   "Where in.wig is in one of the ascii wiggle formats, but not including track lines\n"
   "and chrom.sizes is two column: <chromosome name> <size in bases>\n"
   "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"
-  "   -clipDontDie - If set just issue warning messages rather than dying if wig\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},
-   {"clipDontDie", OPTION_BOOLEAN},
+   {"clip", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void wigToBigWig(char *inName, char *chromSizes, char *outName)
 /* wigToBigWig - Convert ascii format wig file (in fixedStep, variableStep or bedGraph format) 
  * to binary big wig format.. */
 {
 bigWigFileCreate(inName, chromSizes, blockSize, itemsPerSlot, clipDontDie, outName);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 blockSize = optionInt("blockSize", blockSize);
 itemsPerSlot = optionInt("itemsPerSlot", itemsPerSlot);
-clipDontDie = optionExists("clipDontDie");
+clipDontDie = optionExists("clip");
 if (argc != 4)
     usage();
 wigToBigWig(argv[1], argv[2], argv[3]);
 return 0;
 }