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

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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
author mvdbeek
date Mon, 05 Dec 2016 09:58:47 -0500
parents 28d1a6f8143f
children
comparison
equal deleted inserted replaced
20:6e02b9179a24 21:9672fe07a232
8 while(<in>) 8 while(<in>)
9 { 9 {
10 chomp; 10 chomp;
11 my @f=split/\t/,$_,12; 11 my @f=split/\t/,$_,12;
12 ## read number 1 or 2 12 ## read number 1 or 2
13 my ($rnum)=$f[1]=~/(\d)$/; 13 #my ($rnum)=$f[1]=~/(\d)$/;
14 my $rnum=1;
15 if (($f[1] & 128) == 128) {$rnum=2;}
14 16
15 ## XT:A:* 17 ## XT:A:*
16 my ($xt)=$f[11]=~/XT:A:(.)/; 18 my ($xt)=$f[11]=~/XT:A:(.)/;
17 19
18 my $strand="+"; 20 my $strand="+";
19 21
20 ## parse CIGAR 22 ## parse CIGAR
21 if(($f[1]=~/R/)&&($f[8] > $ARGV[1])&&($f[8] <= 10000)) 23 if((($f[1] & 32) == 32)&&($f[8] > $ARGV[1])&&($f[8] <= 10000))
22 { 24 {
23 # CIGAR 25 # CIGAR
24 my (@cigar_m)=$f[5]=~/(\d+)M/g; 26 my (@cigar_m)=$f[5]=~/(\d+)M/g;
25 my (@cigar_d)=$f[5]=~/(\d+)D/g; 27 my (@cigar_d)=$f[5]=~/(\d+)D/g;
26 my (@cigar_s)=$f[5]=~/(\d+)S/g; 28 my (@cigar_s)=$f[5]=~/(\d+)S/g;