cf848a6f3c75bdb85e7030779e193fe837020566
braney
  Mon Mar 16 08:47:34 2020 -0700
Add version numbers to wigToBig and bedGraphToBigWig, and increment the
version number for bedToBigBed since we've made some changes without
incrementing it. refs #25163

diff --git src/utils/bedToBigBed/bedToBigBed.c src/utils/bedToBigBed/bedToBigBed.c
index d01e772..de134fd 100644
--- src/utils/bedToBigBed/bedToBigBed.c
+++ src/utils/bedToBigBed/bedToBigBed.c
@@ -6,54 +6,55 @@
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "dystring.h"
 #include "obscure.h"
 #include "asParse.h"
 #include "basicBed.h"
 #include "sig.h"
 #include "rangeTree.h"
 #include "zlibFace.h"
 #include "sqlNum.h"
 #include "bPlusTree.h"
 #include "bigBed.h"
 #include "twoBit.h"
 
-char *version = "2.7";
+char *version = "2.8";   // when changing, change in bedToBigBed, bedGraphToBigWig, and wigToBigWig
 /* Version history from 2.6 on at least -
+ *   2.8 - Various changes where developer didn't increment version id
  *   2.7 - Added check for duplicate field names in asParse.c
  *   2.6 - Made it not crash on empty input.  
  *   */
 
 /* Things set directly or indirectly by command lne in main() routine. */
 int blockSize = 256;
 int itemsPerSlot = 512;
 char *extraIndex = NULL;
 int bedN = 0;   /* number of standard bed fields */
 int bedP = 0;   /* number of bed plus fields */
 char *asFile = NULL;
 char *asText = NULL;
 char *udcDir = NULL;
 static boolean doCompress = FALSE;
 static boolean tabSep = FALSE;
 static boolean sizesIs2Bit = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
-  "bedToBigBed v. %s - Convert bed file to bigBed. (BigBed version: %d)\n"
+  "bedToBigBed v. %s - Convert bed file to bigBed. (bbi 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"