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

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

20:6e02b9179a24

	    }
	}

	if ($mm > 5) {next;}

	my ($rnum)=$f[1]=~/(\d)$/;
	# CIGAR
	my (@cigar_m)=$f[5]=~/(\d+)M/g;
	my (@cigar_d)=$f[5]=~/(\d+)D/g;
	my (@cigar_s)=$f[5]=~/(\d+)S/g;
	my (@cigar_i)=$f[5]=~/(\d+)I/g;
	my $aln_ln=sum(@cigar_m,@cigar_d);
	
	my $strand="+";
	if($f[1]=~/r/)
	{
	    my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna');
	    $f[9]=$seq->revcom->seq;
	    $strand="-";
	}

21:9672fe07a232

	    }
	}

	if ($mm > 5) {next;}

	#my ($rnum)=$f[1]=~/(\d)$/;
        my $rnum=1;
        if (($f[1] & 128) == 128) {$rnum=2;}

	# CIGAR
	my (@cigar_m)=$f[5]=~/(\d+)M/g;
	my (@cigar_d)=$f[5]=~/(\d+)D/g;
	my (@cigar_s)=$f[5]=~/(\d+)S/g;
	my (@cigar_i)=$f[5]=~/(\d+)I/g;
	my $aln_ln=sum(@cigar_m,@cigar_d);
	
	my $strand="+";
	if(($f[1] & 16) == 16)
	{
	    my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna');
	    $f[9]=$seq->revcom->seq;
	    $strand="-";
	}