--- a/flexbar.pl	Tue Jul 03 07:36:49 2018 -0400
+++ b/flexbar.pl	Tue Jul 03 07:37:31 2018 -0400
@@ -10,13 +10,15 @@
 my @inFiles;
 my @outFiles;
 
+my $compression = "";
+
 foreach(0..$#ARGV){
 	my $arg = $ARGV[$_];
 	
 	if($arg =~ /\.(fastq\w+)$/ || $arg =~ /\.(fastq\w+\.gz)$/ || $arg =~ /\.(fastq\w+\.bz2)$/){
 		
 		if(defined $format && $format ne $1){
-			print STDERR "Paired read files should have the same format.\n";
+			warn "Read files should have the same format.\n";
 			exit 1;
 		}
 		$format = $1;
@@ -27,29 +29,58 @@
 		$arg =~ s/\.fastq\w+\.gz$/\.fastq\.gz/;
 		$arg =~ s/\.fastq\w+\.bz2$/\.fastq\.bz2/;
 		
-		push @inFiles,  $arg if $arg =~ /\.dat_input\.fastq$/ || $arg =~ /\.dat_input\.fastq\.gz$/ || $arg =~ /\.dat_input\.fastq\.bz2$/;
-		push @outFiles, $arg if $arg =~ /\.dat\.fastq$/       || $arg =~ /\.dat\.fastq\.gz$/       || $arg =~ /\.dat\.fastq\.bz2$/;
+		$compression = "GZ"  if $arg =~ /\.fastq\.gz$/;
+		$compression = "BZ2" if $arg =~ /\.fastq\.bz2$/;
 		
 		$ARGV[$_] = $arg;
-		rename $file, $arg;
+		
+		if($arg =~ /\.dat_input\w\.fastq$/ || $arg =~ /\.dat_input\w\.fastq\.gz$/ || $arg =~ /\.dat_input\w\.fastq\.bz2$/){
+			push @inFiles, $arg;
+			rename $file, $arg;
+		}
+		
+		push @outFiles, $arg if $arg =~ /\.dat\.fastq$/ || $arg =~ /\.dat\.fastq\.gz$/ || $arg =~ /\.dat\.fastq\.bz2$/;
 	}
 }
 
-my $call = join " ", @ARGV;
+my $barcoded = 0;
+
+$barcoded = 1 if $ARGV[$#ARGV] =~ /barcoded$/;
+
+my $call = join " ", @ARGV[0..($#ARGV - $barcoded)];
+
+# $call = $call ." --zip-output ". $compression if $barcoded && $compression ne "";
 
 system $call and exit 1;
 
 
 unlink $_ or warn "Could not unlink $_: $!" foreach(@inFiles);
 
-foreach(@outFiles){
-	
-	my $file = $_;
+if($barcoded){
+	$format =~ s/\.gz//;
+	$format =~ s/\.bz2//;
 	
-	s/\.fastq$//;
-	s/\.fastq\.gz$//;
-	s/\.fastq\.bz2$//;
-	
-	rename $file, $_;
+	foreach(<$ARGV[$#ARGV]/flexbarOut*.fastq*>){
+		
+		my $file = $_;
+		
+		s/fastq$/$format/;
+		# s/fastq\.gz$/$format/;
+		# s/fastq\.bz2$/$format/;
+		
+		rename $file, $_;
+	}
+}
+else{
+	foreach(@outFiles){
+		
+		my $file = $_;
+		
+		s/\.fastq$//;
+		s/\.fastq\.gz$//;
+		s/\.fastq\.bz2$//;
+		
+		rename $file, $_;
+	}
 }