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

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

20:6e02b9179a24

	$b[0]=$c[0];
	$c[0]=$swap;
    }
    my $lower=$b[0]-$frag;
    my $upper=$c[0]+$frag;
    system("samtools view -Xf 0x2 $title $a[0]\:$lower\-$upper > temp.sam");
    
    open in,"temp.sam";
    my %ps=();
    my %me=();
    my $ref_sup=0;

    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:(.)/;
	
	## Coordinate
	if ($f[1]=~/r/)
	{
	    my (@cigar_m)=$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;

21:9672fe07a232

	$b[0]=$c[0];
	$c[0]=$swap;
    }
    my $lower=$b[0]-$frag;
    my $upper=$c[0]+$frag;
    system("samtools view -f 0x2 $title $a[0]\:$lower\-$upper > temp.sam");
    
    open in,"temp.sam";
    my %ps=();
    my %me=();
    my $ref_sup=0;

    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:(.)/;
	
	## Coordinate
	if (($f[1] & 16) == 16)
	{
	    my (@cigar_m)=$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;