--- a/miRPlant.pl	Wed Dec 03 02:03:27 2014 -0500
+++ b/miRPlant.pl	Fri Dec 05 00:11:02 2014 -0500
@@ -17,7 +17,7 @@
 #use Term::ANSIColor;
 
 my %opts;
-GetOptions(\%opts,"i:s@","tag:s@","format=s","gfa=s","pre=s","mat=s","rfam:s","dis:i","flank:i","mfe:f","idx:s","idx2:s","mis:i","r:i","v:i","e:i","f:i","a:s","M:i","t:i","min:i","max:i","o:s","path:s","D","h");
+GetOptions(\%opts,"i:s@","tag:s@","phred:i","format=s","gfa=s","pre=s","mat=s","rfam:s","dis:i","flank:i","mfe:f","idx:s","idx2:s","mis:i","r:i","v:i","e:i","f:i","a:s","M:i","t:i","min:i","max:i","o:s","path:s","D","h");
 if (!(defined $opts{i} and defined $opts{format} and defined $opts{gfa} and defined $opts{pre} and defined $opts{mat}) || defined $opts{h}) { #necessary arguments
 &usage;
 }
@@ -33,7 +33,9 @@
 }
 
 my $phred_qv=64;
-
+if (defined $opts{'phred'}) {
+	$phred_qv=$opts{'phred'};
+}
 
 my @inputfiles=@{$opts{'i'}};
 my @inputtags=@{$opts{'tag'}};