01089c81628328a3a9083680e1705238e4246472
braney
  Mon Oct 2 15:45:51 2023 -0700
tweak usage message to explain that relaxation of sorting requirement

diff --git src/utils/bedToBigBed/bedToBigBed.c src/utils/bedToBigBed/bedToBigBed.c
index 33d5831..a8dd192 100644
--- src/utils/bedToBigBed/bedToBigBed.c
+++ src/utils/bedToBigBed/bedToBigBed.c
@@ -68,32 +68,33 @@
   "\n"
   "The chrom.sizes file may also be a chromAlias bigBed file, or a URL to\n"
   "such a file, by specifying the -sizesIsChromAliasBb option.  When using\n"
   "a chromAlias bigBed file, the input BED file may have chromosome names\n"
   "matching any of the sequence name aliases in the chromAlias file.\n"
   "\n"
   "For UCSC provided genomes, the chromAlias files can be found under:\n"
   "    https://hgdownload.soe.ucsc.edu/goldenPath/<db>/bigZips/<db>.chromAlias.bb\n"
   "For UCSC GenArk assembly hubs, the chrom aliases are namedd in the form:\n"
   "    https://hgdownload.soe.ucsc.edu/hubs/GCF/006/542/625/GCF_006542625.1/GCF_006542625.1.chromAlias.bb\n"
   "For a description of generating chromAlias files for your own assembly hub, see:\n"
   "      http://genomewiki.ucsc.edu/index.php/Chrom_Alias\n"
   "\n"
   "The in.bed file must be sorted by chromosome,start,\n"
   "  to sort a bed file, use the unix sort command:\n"
-  "     LC_ALL=C sort -k1,1 -k2,2n unsorted.bed > sorted.bed\n"
-  "Sorting must be set to skip Unicode mapping to make it case-sensitive (LC_ALL=C).\n"
+  "     sort -k1,1 -k2,2n unsorted.bed > sorted.bed\n"
+  "Sequences must be sorted by name so all sequences with the same name\n"
+  "are collected together, but they don't need to be in any particular order.\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"