diff scripts/pickUniqPairFastq_MEM.pl @ 12:ca36262102d8 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50

--- a/scripts/pickUniqPairFastq_MEM.pl	Thu Apr 28 07:57:12 2016 -0400
+++ b/scripts/pickUniqPairFastq_MEM.pl	Fri Apr 29 05:47:54 2016 -0400
@@ -30,13 +30,13 @@
 		$xs=$a[$i];
 	    }
 	    if (($xs > 0) && ($as-$xs <= $ARGV[2])) {$xt="R";}
-	    else {$xt="U";}
+	    elsif ($as > 0) {$xt="U";}
 	}
 
 	## revcom the read mapped to the reverse strand
 	if($f[1]=~/r/)
 	{
-		my $seq=Bio::Seq->new(-seq=>$f[9]);
+		my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna');
 		$f[9]=$seq->revcom->seq;
 		$f[10]=reverse $f[10];
 	}