comparison scripts/pickUniqPos_MEM.pl @ 12:ca36262102d8 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50

11:e19d9742c99b

            elsif ($a[$i] =~ /^XS:i:/) {
                $a[$i] =~ s/XS:i://;
                $xs=$a[$i];
            }
            if (($xs > 0) && ($as-$xs <= $ARGV[1])) {$xt="R";}
            else {$xt="U";}
        }

	my $strand="+";
	## revcomp
	if($f[1]=~/r/)
        {
                my $seq=Bio::Seq->new(-seq=>$f[9]);
                $f[9]=$seq->revcom->seq;
		$strand="-";
        }

	## parse CIGAR

12:ca36262102d8

            elsif ($a[$i] =~ /^XS:i:/) {
                $a[$i] =~ s/XS:i://;
                $xs=$a[$i];
            }
            if (($xs > 0) && ($as-$xs <= $ARGV[1])) {$xt="R";}
            elsif ($as > 0) {$xt="U";}
        }

	my $strand="+";
	## revcomp
	if($f[1]=~/r/)
        {
                my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna');
                $f[9]=$seq->revcom->seq;
		$strand="-";
        }

	## parse CIGAR