87c907ef671a3f51d3a5dc361f8b7446499171f4
markd
  Fri Sep 9 11:12:34 2022 -0700
improved wording for of bedToBigBed help per Max's suggestion

diff --git src/utils/bedToBigBed/bedToBigBed.c src/utils/bedToBigBed/bedToBigBed.c
index f601d30..967e596 100644
--- src/utils/bedToBigBed/bedToBigBed.c
+++ src/utils/bedToBigBed/bedToBigBed.c
@@ -53,33 +53,33 @@
   "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"
   "\n"
   "If the assembly <db> is hosted by UCSC, chrom.sizes can be a URL like\n"
   "  http://hgdownload.soe.ucsc.edu/goldenPath/<db>/bigZips/<db>.chrom.sizes\n"
   "or you may use the script fetchChromSizes to download the chrom.sizes file.\n"
   "If you have bed annotations on patch sequences from NCBI, a more inclusive\n"
   "chrom.sizes file can be found using a URL like\n"
   "  http://hgdownload.soe.ucsc.edu/goldenPath/<db>/database/chromInfo.txt.gz\n"
   "If not hosted by UCSC, a chrom.sizes file can be generated by running\n"
   "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.  With a\n"
-  "chromAlias, the input BED file may have chromosome names matching any\n"
-  "of the sequence name aliases in the chromAlias file.\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"
   "     sort -k1,1 -k2,2n unsorted.bed > sorted.bed\n"
   "Sorting must be set to skip Unicode mapping (LC_COLLATE=C).\n"
   "\n"
   "options:\n"
   "   -type=bedN[+[P]] : \n"