Mercurial > repos > portiahollyoak > temp

diff scripts/pickUniqMate.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 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;