Mercurial > repos > portiahollyoak > temp

diff scripts/pickUniqPairFastq.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 e19d9742c99b
children
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--- a/scripts/pickUniqPairFastq.pl	Wed Oct 26 07:24:45 2016 -0400
+++ b/scripts/pickUniqPairFastq.pl	Mon Dec 05 09:58:47 2016 -0500
@@ -13,13 +13,15 @@
 	chomp;
 	my @f=split/\t/,$_,12;
 	## read number 1 or 2
-	my ($rnum)=$f[1]=~/(\d)$/;
+	#my ($rnum)=$f[1]=~/(\d)$/;
+        my $rnum=1;
+        if (($f[1] & 128) == 128) {$rnum=2;}
 
 	## XT:A:* 
 	my ($xt)=$f[11]=~/XT:A:(.)/;
 
 	## revcom the read mapped to the reverse 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;