Mercurial > repos > devteam > pileup_parser

diff pileup_parser.pl @ 2:85bedbea8a12 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser commit ab627176cd4f6efe6d1fe4b85baa679aaa651eb1
author devteam
date Wed, 05 Oct 2016 06:30:36 -0400
parents ff1ba9b75337
children
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--- a/pileup_parser.pl	Tue Jun 03 12:40:39 2014 -0400
+++ b/pileup_parser.pl	Wed Oct 05 06:30:36 2016 -0400
@@ -37,7 +37,7 @@
 	my @fields = split /\t/;
 	next if $fields[ $ref_base_column ] eq "*"; # skip indel lines
  	my $read_bases   = $fields[ $read_bases_column ];
- 	die "Coverage column" . ($cvrg_column+1) . " contains non-numeric values. Check your input parameters as well as format of input dataset." if ( not isdigit $fields[ $cvrg_column ] );
+ 	die "Coverage column" . ($cvrg_column+1) . " contains non-numeric values. Check your input parameters as well as format of input dataset." if ( not $fields[ $cvrg_column ] =~ qr/^[[:digit:]]+$/x );
     next if $fields[ $cvrg_column ] < $cvrg_cutoff;
 	my $base_quality = $fields[ $base_quality_column ];
 	if ($read_bases =~ m/[\$\^\+-]/) {