comparison pileup_parser.pl @ 2:ffeb59f7a82d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser commit ab627176cd4f6efe6d1fe4b85baa679aaa651eb1

1:d31417e25765

	chop;
	next if m/^\#/;
	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 ] );
    next if $fields[ $cvrg_column ] < $cvrg_cutoff;
	my $base_quality = $fields[ $base_quality_column ];
	if ($read_bases =~ m/[\$\^\+-]/) {
		$read_bases =~ s/\^.//g; #removing the start of the read segement mark
		$read_bases =~ s/\$//g; #removing end of the read segment mark

2:ffeb59f7a82d

	chop;
	next if m/^\#/;
	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 $fields[ $cvrg_column ] =~ qr/^[[:digit:]]+$/x );
    next if $fields[ $cvrg_column ] < $cvrg_cutoff;
	my $base_quality = $fields[ $base_quality_column ];
	if ($read_bases =~ m/[\$\^\+-]/) {
		$read_bases =~ s/\^.//g; #removing the start of the read segement mark
		$read_bases =~ s/\$//g; #removing end of the read segment mark