f2049f3064f288aeebed2d88a0123e48389eda4c
angie
  Wed Apr 1 15:31:40 2015 -0700
Updating usage message in utils that now accept a URL for chrom.sizes.
resolves #14857

diff --git src/utils/bedGraphToBigWig/bedGraphToBigWig.c src/utils/bedGraphToBigWig/bedGraphToBigWig.c
index f59b61f..8115a24 100644
--- src/utils/bedGraphToBigWig/bedGraphToBigWig.c
+++ src/utils/bedGraphToBigWig/bedGraphToBigWig.c
@@ -24,34 +24,37 @@
 static int itemsPerSlot = 1024;
 static boolean doCompress = FALSE;
 static int maxGigs = 100;   // Maximum number of gigs to allocate in one block.  
 			    // Undocumented on purpose.
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bedGraphToBigWig v %d - Convert a bedGraph file to bigWig format.\n"
   "usage:\n"
   "   bedGraphToBigWig in.bedGraph chrom.sizes out.bw\n"
   "where in.bedGraph is a four column file in the format:\n"
   "      <chrom> <start> <end> <value>\n"
-  "and chrom.sizes is two column: <chromosome name> <size in bases>\n"
+  "and chrom.sizes is a two-column file/URL: <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"
+  "If the assembly <db> is hosted by UCSC, chrom.sizes can be a URL like\n"
+  "  http://hgdownload.cse.ucsc.edu/goldenPath/<db>/bigZips/<db>.chrom.sizes\n"
+  "or you may use the script fetchChromSizes to download the chrom.sizes file.\n"
+  "If not hosted by UCSC, a chrom.sizes file can be generated by running\n"
+  "twoBitInfo on the assembly .2bit file.\n"
   "The input bedGraph file must be sorted, use the unix sort command:\n"
   "  sort -k1,1 -k2,2n unsorted.bedGraph > sorted.bedGraph\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"
   "   -unc - If set, do not use compression."
   , bbiCurrentVersion, blockSize, itemsPerSlot
   );
 }
 
 static struct optionSpec options[] = {
    {"blockSize", OPTION_INT},
    {"itemsPerSlot", OPTION_INT},
    {"unc", OPTION_BOOLEAN},
    {"maxGigs", OPTION_INT},