916f0b7ad3bfd70ae91ecdb4c30ccfc67094a015
braney
  Sun May 24 14:06:04 2015 -0700
make sure that chroms are sorted in a case-sensitive manner in
bedToBigBed because otherwise the indexes don't work #15400

diff --git src/utils/bedToBigBed/bedToBigBed.c src/utils/bedToBigBed/bedToBigBed.c
index 6324cb3..988355e 100644
--- src/utils/bedToBigBed/bedToBigBed.c
+++ src/utils/bedToBigBed/bedToBigBed.c
@@ -40,30 +40,31 @@
 errAbort(
   "bedToBigBed v. %s - Convert bed file to bigBed. (BigBed version: %d)\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 a two-column file/URL: <chromosome name> <size in bases>\n"
   "and out.bb is the output indexed big bed file.\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 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"
+  "Sorting must be case insensitive (LC_COLLATE=C).\n"
   "\n"
   "options:\n"
   "   -type=bedN[+[P]] : \n"
   "                      N is between 3 and 15, \n"
   "                      optional (+) if extra \"bedPlus\" fields, \n"
   "                      optional P specifies the number of extra fields. Not required, but preferred.\n"
   "                      Examples: -type=bed6 or -type=bed6+ or -type=bed6+3 \n"
   "                      (see http://genome.ucsc.edu/FAQ/FAQformat.html#format1)\n"
   "   -as=fields.as - If you have non-standard \"bedPlus\" fields, it's great to put a definition\n"
   "                   of each field in a row in AutoSql format here.\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.\n"
   "   -tab - If set, expect fields to be tab separated, normally\n"
   "           expects white space separator.\n"