32caec3dbd6130357867cf65a101ee4757f7c259
jnavarr5
  Wed Jul 24 16:04:17 2019 -0700
Adding a note about how to find the most up-to-date chrom.sizes file for an assembly with patch sequences, no Redmine.

diff --git src/utils/bedToBigBed/bedToBigBed.c src/utils/bedToBigBed/bedToBigBed.c
index 6fe2795..d01e772 100644
--- src/utils/bedToBigBed/bedToBigBed.c
+++ src/utils/bedToBigBed/bedToBigBed.c
@@ -38,30 +38,33 @@
 static boolean sizesIs2Bit = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 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.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.\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"
   "                      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"