add -x ... which adds extra fields... so far just gene name

clipper/gtf2bed

@@ -23,6 +23,10 @@
 # ALSO, IT WOULD BE NICE IF YOU LET ME KNOW YOU USED IT.
 
 use Data::Dumper;
+use Getopt::Long;
+
+my $extended;
+GetOptions("x"=>\$extended);
 
 $in = shift @ARGV;
 
@@ -105,8 +109,15 @@ for $id (
 		my $exst = join ",", map {$_->[3]-$beg-1} @ex;				# exon start
 		my $exsz = join ",", map {$_->[4]-$_->[3]+1} @ex;			# exon size
 
+        my $gene_id;
+        my $extend = "";
+        if ($extended) {
+    	    ($gene_id) = $attr =~ /gene_name "([^"]+)"/;
+    	    ($gene_id) = $attr =~ /gene_id "([^"]+)"/ unless $gene_id;
+            $extend="\t$gene_id";
+        }
 		# added an extra comma to make it look exactly like ucsc's beds
-		print "$chr\t$beg\t$end\t$id\t0\t$dir\t$cds\t$cde\t0\t$exn\t$exsz,\t$exst,\n";
+		print "$chr\t$beg\t$end\t$id\t0\t$dir\t$cds\t$cde\t0\t$exn\t$exsz,\t$exst,$extend\n";
 }