b3df809057789bbfe8bfb731aac4961d4bf9191e
hiram
  Mon Jan 11 13:00:50 2016 -0800
add usage note of how to use awk to run up a featureBits measurement no redmine

diff --git src/utils/bedSingleCover.pl src/utils/bedSingleCover.pl
index ffc7dbd..51da908 100755
--- src/utils/bedSingleCover.pl
+++ src/utils/bedSingleCover.pl
@@ -4,30 +4,34 @@
 
 # DO NOT EDIT the /cluster/bin/scripts copy of this file --
 # edit ~/kent/src/utils/bedSingleCover.pl instead.
 
 use strict;
 use warnings;
 
 my $argc = scalar(@ARGV);
 
 if ($argc < 1) {
     printf STDERR "usage: bedSingleCover.pl [file.bed] > singleCover.bed\n";
     printf STDERR "will combine overlapping bed elements into one element\n";
     printf STDERR "No need to pre-sort the bed file, it will be sorted here\n";
     printf STDERR "result is four columns: chr start end size\n";
     printf STDERR "where size is the size of the element: size=end-start\n";
+    printf STDERR "\nTo obtain a quick featureBits like measurement of\n";
+    printf STDERR "this singleCover result, using awk:\n";
+    printf STDERR " bedSingleCover.pl file.bed |";
+    printf STDERR " awk '{sum+=\$3-\$2}END{printf \"%%d bases\\n\", sum}'\n";
     exit 255
 }
 
 my $bedFile = shift;
 my $chr = "";
 my $prevEnd = 0;
 my $start = 0;
 my $end = 0;
 my $size = 0;
 if ($bedFile =~ m/^stdin$/) {
   open (FH, "grep -v '^ *#' /dev/stdin | sort -k1,1 -k2,2n |") or die "can not read /dev/stdin";
 } else {
   open (FH, "grep -v '^ *#' $bedFile | sort -k1,1 -k2,2n|") or die "can not read $bedFile";
 }
 while (my $line = <FH>) {