62ee6828ceb79fcea5fc5058b6ec6184c175c758
braney
  Tue Sep 27 13:00:50 2011 -0700
fix per Jim.. a more clear usage message
diff --git src/utils/bedToBigBed/bedToBigBed.c src/utils/bedToBigBed/bedToBigBed.c
index 1efef18..154243d 100644
--- src/utils/bedToBigBed/bedToBigBed.c
+++ src/utils/bedToBigBed/bedToBigBed.c
@@ -33,30 +33,31 @@
   "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"
   "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"
   "           expects white space separator.\n"
   , bbiCurrentVersion, blockSize, itemsPerSlot
   );
 }
 
 static struct optionSpec options[] = {
    {"blockSize", OPTION_INT},
    {"itemsPerSlot", OPTION_INT},
    {"bedFields", OPTION_INT},
    {"rgbField", OPTION_INT},
    {"as", OPTION_STRING},
    {"unc", OPTION_BOOLEAN},
    {"tabs", OPTION_BOOLEAN},