f2049f3064f288aeebed2d88a0123e48389eda4c
angie
  Wed Apr 1 15:31:40 2015 -0700
Updating usage message in utils that now accept a URL for chrom.sizes.
resolves #14857

diff --git src/utils/bedClip/bedClip.c src/utils/bedClip/bedClip.c
index 2618a31..1b67d59 100644
--- src/utils/bedClip/bedClip.c
+++ src/utils/bedClip/bedClip.c
@@ -6,30 +6,36 @@
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "bbiFile.h"
 #include "sqlNum.h"
 #include "obscure.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bedClip - Remove lines from bed file that refer to off-chromosome places.\n"
   "usage:\n"
   "   bedClip input.bed chrom.sizes output.bed\n"
+  "chrom.sizes is a two-column file/URL: <chromosome name> <size in bases>\n"
+  "If the assembly <db> is hosted by UCSC, chrom.sizes can be a URL like\n"
+  "  http://hgdownload.cse.ucsc.edu/goldenPath/<db>/bigZips/<db>.chrom.sizes\n"
+  "or you may use the script fetchChromSizes to download the chrom.sizes file.\n"
+  "If not hosted by UCSC, a chrom.sizes file can be generated by running\n"
+  "twoBitInfo on the assembly .2bit file.\n"
   "options:\n"
   "   -verbose=2 - set to get list of lines clipped and why\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 void bedClip(char *inFile, char *chromSizes, char *outFile)
 /* bedClip - Remove lines from bed file that refer to off-chromosome places.. */
 {
 struct hash *chromSizesHash = bbiChromSizesFromFile(chromSizes);
 struct lineFile *lf = lineFileOpen(inFile, TRUE);
 FILE *f = mustOpen(outFile, "w");