74083f96c749e637befe819c250e79b0a0ba378a
hiram
  Wed Feb 8 11:25:29 2012 -0800
mention fetchChromSizes in these usage messages, redmine 6844
diff --git src/utils/wigToBigWig/wigToBigWig.c src/utils/wigToBigWig/wigToBigWig.c
index ef8fedd..deafc7a 100644
--- src/utils/wigToBigWig/wigToBigWig.c
+++ src/utils/wigToBigWig/wigToBigWig.c
@@ -1,68 +1,70 @@
 /* wigToBigWig - Convert ascii format wig file (in fixedStep, variableStep or bedGraph format) 
  * to binary big wig format.. */
 #include "common.h"
 #include "obscure.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "bigWig.h"
 #include "bwgInternal.h"
 #include "zlibFace.h"
 
 
 static int blockSize = 256;
 static int itemsPerSlot = 1024;
 static boolean clipDontDie = FALSE;
 static boolean doCompress = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "wigToBigWig v %d - Convert ascii format wig file (in fixedStep, variableStep\n"
   "or bedGraph 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"
+  "Use the script: fetchChromSizes to obtain the actual chrom.sizes information\n"
+  "from UCSC, please do not make up a chrom sizes from your own information.\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.\n"
   "   -unc - If set, do not use compression."
   , bbiCurrentVersion, blockSize, itemsPerSlot
   );
 }
 
 static struct optionSpec options[] = {
    {"blockSize", OPTION_INT},
    {"itemsPerSlot", OPTION_INT},
    {"clip", OPTION_BOOLEAN},
    {"unc", 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, doCompress, outName);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 blockSize = optionInt("blockSize", blockSize);
 itemsPerSlot = optionInt("itemsPerSlot", itemsPerSlot);
 clipDontDie = optionExists("clip");
 doCompress = !optionExists("unc");
 if (argc != 4)
     usage();
 wigToBigWig(argv[1], argv[2], argv[3]);
 if (verboseLevel() > 1)
     printVmPeak();
 return 0;
 }