2494776c2d9c80308c307ebcd7fe074fadebcafe
max
  Mon Nov 28 18:33:32 2011 -0800
added -k1,1 to sort options in help message, sort alone doesn't work
diff --git src/hg/bedItemOverlapCount/bedItemOverlapCount.c src/hg/bedItemOverlapCount/bedItemOverlapCount.c
index e30a567..eb7efa8 100644
--- src/hg/bedItemOverlapCount/bedItemOverlapCount.c
+++ src/hg/bedItemOverlapCount/bedItemOverlapCount.c
@@ -43,33 +43,33 @@
     {"password", OPTION_STRING},
     {"max", OPTION_BOOLEAN},
     {"zero", OPTION_BOOLEAN},
     {"bed12", OPTION_BOOLEAN},
     {"outBounds", OPTION_BOOLEAN},
     {NULL, 0}
 };
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bedItemOverlapCount - count number of times a base is overlapped by the\n"
   "\titems in a bed file.  Output is bedGraph 4 to stdout.\n"
   "usage:\n"
-  " sort bedFile.bed | bedItemOverlapCount [options] <database> stdin\n"
+  " sort -k1,1 bedFile.bed | bedItemOverlapCount [options] <database> stdin\n"
   "To create a bigWig file from this data to use in a custom track:\n"
-  " sort bedFile.bed | bedItemOverlapCount [options] <database> stdin \\\n"
+  " sort -k1,1 bedFile.bed | bedItemOverlapCount [options] <database> stdin \\\n"
   "         > bedFile.bedGraph\n"
   " bedGraphToBigWig bedFile.bedGraph chrom.sizes bedFile.bw\n"
   "   where the chrom.sizes is obtained with the script: fetchChromSizes\n"
   "   See also:\n"
   " http://genome-test.cse.ucsc.edu/~kent/src/unzipped/utils/userApps/fetchChromSizes\n"
   "options:\n"
   "   -zero      add blocks with zero count, normally these are ommitted\n"
   "   -bed12     expect bed12 and count based on blocks\n"
   "              Without this option, only the first three fields are used.\n"
   "   -max       if counts per base overflows set to max (%lu) instead of exiting\n"
   "   -outBounds output min/max to stderr\n"
   "   -chromSize=sizefile\tRead chrom sizes from file instead of database\n"
   "             sizefile contains two white space separated fields per line:\n"
   "		chrom name and size\n"
   "   -host=hostname\tmysql host used to get chrom sizes\n"