74083f96c749e637befe819c250e79b0a0ba378a
hiram
  Wed Feb 8 11:25:29 2012 -0800
mention fetchChromSizes in these usage messages, redmine 6844
diff --git src/utils/bedToBigBed/bedToBigBed.c src/utils/bedToBigBed/bedToBigBed.c
index a868ee3..3f870eb 100644
--- src/utils/bedToBigBed/bedToBigBed.c
+++ src/utils/bedToBigBed/bedToBigBed.c
@@ -20,30 +20,32 @@
 int rgbField = 0;
 char *as = NULL;
 static boolean doCompress = FALSE;
 static boolean tabSep = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bedToBigBed v. %d - Convert bed file to bigBed.\n"
   "usage:\n"
   "   bedToBigBed in.bed chrom.sizes out.bb\n"
   "Where in.bed is in one of the ascii bed formats, but not including track lines\n"
   "and chrom.sizes is two column: <chromosome name> <size in bases>\n"
   "and out.bb is the output indexed big bed 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"
   "The in.bed file must be sorted by chromosome,start,\n"
   "  to sort a bed file, use the unix sort command:\n"
   "     sort -k1,1 -k2,2n unsorted.bed > sorted.bed\n"
   "\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"
   "   -bedFields=N - Number of fields that fit standard bed definition.  If undefined\n"
   "                  assumes all fields in bed are defined.\n"
   "   -as=fields.as - If have non-standard fields, it's great to put a definition\n"
   "                   of each field in a row in AutoSql format here.\n"
   "   -rgbField=N  - the Nth field is a comma separated R,G,B triple.\n"
   "                  For the usual itemRgb/reserved bed field this is 9.\n"
   "   -unc - If set, do not use compression.\n"
   "   -tabs - If set, expect fields to be tab separated, normally\n"