comparison scripts/pickUniqPairFastq.pl @ 21:9672fe07a232 draft default tip

planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty

20:6e02b9179a24

while(<in>)
{
	chomp;
	my @f=split/\t/,$_,12;
	## read number 1 or 2
	my ($rnum)=$f[1]=~/(\d)$/;

	## XT:A:* 
	my ($xt)=$f[11]=~/XT:A:(.)/;

	## 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];
	}

21:9672fe07a232

while(<in>)
{
	chomp;
	my @f=split/\t/,$_,12;
	## read number 1 or 2
	#my ($rnum)=$f[1]=~/(\d)$/;
        my $rnum=1;
        if (($f[1] & 128) == 128) {$rnum=2;}

	## XT:A:* 
	my ($xt)=$f[11]=~/XT:A:(.)/;

	## revcom the read mapped to the reverse strand
	if(($f[1] & 16) == 16)
	{
		my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna');
		$f[9]=$seq->revcom->seq;
		$f[10]=reverse $f[10];
	}