8a7fe87bf9ffd7fc1038c9d85984955afb82f0dc
gperez2
  Thu Feb 20 17:06:31 2025 -0800
Updating the bedToBigBed help message and error output for the new sort option, refs #29104

diff --git src/utils/bedToBigBed/bedToBigBed.c src/utils/bedToBigBed/bedToBigBed.c
index dee366af81e..70391d120aa 100644
--- src/utils/bedToBigBed/bedToBigBed.c
+++ src/utils/bedToBigBed/bedToBigBed.c
@@ -67,32 +67,32 @@
   "twoBitInfo on the assembly .2bit file or the 2bit file or used directly\n"
   "if the -sizesIs2Bit option is specified.\n"
   "\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"
-  "Without the -sort option the in.bed file must be sorted by chromosome,start,\n"
-  "  to sort a bed file, use the unix sort command:\n"
+  "Without the -sort option, the in.bed file must be sorted by the chromosome and start fields.\n"
+  "  To sort a BED file, you can use bedSort or the following Unix command:\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"