comparison scripts/pickUniqPairFastq_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 <= $ARGV[2])) {$xt="R";}
	    else {$xt="U";}
	}

	## revcom the read mapped to the reverse strand
	if($f[1]=~/r/)
	{
		my $seq=Bio::Seq->new(-seq=>$f[9]);
		$f[9]=$seq->revcom->seq;
		$f[10]=reverse $f[10];
	}
	if (($rnum == 1) || ($rnum == 2))
	{

12:ca36262102d8

	    elsif ($a[$i] =~ /^XS:i:/) {
		$a[$i] =~ s/XS:i://;
		$xs=$a[$i];
	    }
	    if (($xs > 0) && ($as-$xs <= $ARGV[2])) {$xt="R";}
	    elsif ($as > 0) {$xt="U";}
	}

	## revcom the read mapped to the reverse strand
	if($f[1]=~/r/)
	{
		my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna');
		$f[9]=$seq->revcom->seq;
		$f[10]=reverse $f[10];
	}
	if (($rnum == 1) || ($rnum == 2))
	{