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comparison 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
comparison
equal deleted inserted replaced
1:1670f0565000 2:85bedbea8a12
35 chop; 35 chop;
36 next if m/^\#/; 36 next if m/^\#/;
37 my @fields = split /\t/; 37 my @fields = split /\t/;
38 next if $fields[ $ref_base_column ] eq "*"; # skip indel lines 38 next if $fields[ $ref_base_column ] eq "*"; # skip indel lines
39 my $read_bases = $fields[ $read_bases_column ]; 39 my $read_bases = $fields[ $read_bases_column ];
40 die "Coverage column" . ($cvrg_column+1) . " contains non-numeric values. Check your input parameters as well as format of input dataset." if ( not isdigit $fields[ $cvrg_column ] ); 40 die "Coverage column" . ($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 );
41 next if $fields[ $cvrg_column ] < $cvrg_cutoff; 41 next if $fields[ $cvrg_column ] < $cvrg_cutoff;
42 my $base_quality = $fields[ $base_quality_column ]; 42 my $base_quality = $fields[ $base_quality_column ];
43 if ($read_bases =~ m/[\$\^\+-]/) { 43 if ($read_bases =~ m/[\$\^\+-]/) {
44 $read_bases =~ s/\^.//g; #removing the start of the read segement mark 44 $read_bases =~ s/\^.//g; #removing the start of the read segement mark
45 $read_bases =~ s/\$//g; #removing end of the read segment mark 45 $read_bases =~ s/\$//g; #removing end of the read segment mark