56da8a5745b1ef79c8087ab53e3590e4395d0751
hiram
  Thu May 18 11:34:20 2017 -0700
catch up checkin no redmine

diff --git src/utils/ncbi/createNcbiCytoBand.pl src/utils/ncbi/createNcbiCytoBand.pl
index 6009db9..63c3210 100755
--- src/utils/ncbi/createNcbiCytoBand.pl
+++ src/utils/ncbi/createNcbiCytoBand.pl
@@ -1,48 +1,48 @@
-#!/usr/local/bin/perl
+#!/usr/bin/env perl
 # File: createNcbiCytoBand
 # Author: Terry Furey
 # Date: 11/14/2003
 # Description: Convert NCBI files into cytoBand track
 
 # USAGE message
 if ($#ARGV != 0) {
     print stderr "USAGE: createNcbiCytoBand <ncbi file>\n";
     exit(1);
 }
 $file = shift(@ARGV);
 open(FILE, "$file") || die("Could not open $file\n");
 
 # Read in file and output cytoBand.bed file
 open(OUT, ">cytoBand.bed");
 $prevstart = "";
 $prevend = "";
 while ($line = <FILE>) {
     chomp($line);
     ($chr, $arm, $band, $iscntop, $iscnbot, $start, $end, $stain, $density, @rest) = split("\t",$line); 
     # ignore bogus line at the beginning of each chrom
     if (($start == 0) && ($end == 1)) {
 	$prevend=0;
 	next;
     }
     # Make data 0-based
     if (($start > 0) && ($start > $prevend)) {
 	$start--;
     }
     # the first band on a chrom says it starts at '2' instead of '1'
     # we want zero for that
     $start = 0 if (1 == $start);
     # Checks for observed errors in NCBI file
     if ($start == $prevstart) {
 	$start = $prevend + 1;
     }
     if (!$stain) {
 	$stain = "gneg";
     }
     # Only print lines with band data
     if ($chr =~ /[0-9,X,Y]/) {
 	$band =~ s/\://;
 	print OUT "chr$chr\t$start\t$end\t$arm$band\t$stain$density\n";
     }
     $prevstart = $start;
     $prevend = $end;
 }