--- GFF.pm.old	2005-10-09 11:16:22.000000000 -0400
+++ GFF.pm	2006-01-12 10:44:05.000000000 -0500
@@ -1,4 +1,4 @@
-# GFF.pm,v 1.132.2.1 2005/10/09 15:16:22 jason Exp
+# $Id: GFF.pm,v 1.137 2006/01/11 20:26:25 jason Exp $
 
 =head1 NAME
 
@@ -203,7 +203,7 @@
 
 For annotations that are linked to proteins, this field describes the
 phase of the annotation on the codons.  It is a number from 0 to 2, or
-"." for features that have no phase\.
+"." for features that have no phase.
 
 =item 9. group
 
@@ -1759,7 +1759,7 @@
 
   my $tied_stdin = tied(*STDIN);
   open SAVEIN,"<&STDIN" unless $tied_stdin;
-  local @ARGV = $self->setup_argv($file_or_directory,'gff') or return;  # to play tricks with reader
+  local @ARGV = $self->setup_argv($file_or_directory,'gff','gff3') or return;  # to play tricks with reader
   my $result = $self->do_load_gff('ARGV');
   open STDIN,"<&SAVEIN" unless $tied_stdin;  # restore STDIN
   return $result;
@@ -2222,7 +2222,7 @@
 
   # defaults
   if (!@preferred) {
-    @preferred = $self->{gff3_flag} ? qw(Target Parent ID) : qw(Target Sequence Transcript);
+    @preferred = $self->{load_data}{gff3_flag} ? qw(Target Parent ID) : qw(Target Sequence Transcript);
   }
 
   my %preferred = map {lc($_) => @preferred-$count++} @preferred;
@@ -2389,7 +2389,7 @@
   print STDERR $self->{load_data}{count}," records$lineend" 
     if $self->{__verbose__} && $self->{load_data}{count} % 1000 == 0;
 
-  my ($gclass,$gname,$tstart,$tstop,$attributes) = $self->split_group($group,$self->{gff3_flag});
+  my ($gclass,$gname,$tstart,$tstop,$attributes) = $self->split_group($group,$self->{load_data}{gff3_flag});
 
   # no standard way in the GFF file to denote the class of the reference sequence -- drat!
   # so we invoke the factory to do it