Mercurial > repos > portiahollyoak > temp
diff scripts/pickUniqMate.pl @ 21:9672fe07a232 draft default tip
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
author | mvdbeek |
---|---|
date | Mon, 05 Dec 2016 09:58:47 -0500 |
parents | ca36262102d8 |
children |
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--- a/scripts/pickUniqMate.pl Wed Oct 26 07:24:45 2016 -0400 +++ b/scripts/pickUniqMate.pl Mon Dec 05 09:58:47 2016 -0500 @@ -51,7 +51,10 @@ if ($mm > 5) {next;} - my ($rnum)=$f[1]=~/(\d)$/; + #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; @@ -60,7 +63,7 @@ my $aln_ln=sum(@cigar_m,@cigar_d); my $strand="+"; - if($f[1]=~/r/) + if(($f[1] & 16) == 16) { my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna'); $f[9]=$seq->revcom->seq;