Allow sequences named '0'. See #610, #662

GMOD · Dec 2, 2015 · 2ff5a4a · 2ff5a4a
1 parent 26829a9
commit 2ff5a4a
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Showing 2 changed files with 15 additions and 11 deletions.
diff --git a/src/perl5/Bio/JBrowse/Cmd/IndexNames.pm b/src/perl5/Bio/JBrowse/Cmd/IndexNames.pm
@@ -434,7 +434,7 @@ sub make_operations {
     my ( $self, $record ) = @_;
 
     my $lc_name = lc $record->[0];
-    unless( $lc_name ) {
+    unless( defined $lc_name ) {
         unless( $self->{already_warned_about_blank_name_records} ) {
             warn "WARNING: some blank name records found, skipping.\n";
             $self->{already_warned_about_blank_name_records} = 1;

diff --git a/src/perl5/Bio/JBrowse/FeatureStream.pm b/src/perl5/Bio/JBrowse/FeatureStream.pm
@@ -107,16 +107,20 @@ sub flatten_to_name {
     # rearrange the array of names to be in the order of name_attrs
     @names = @names[ map { exists $namepositions{$_} ? (@{$namepositions{$_}}) : () } @{$self->{name_attrs}} ];
 
-    my @namerec = (
-        \@names,
-        $self->{track_label},
-        $names[0],
-        $f->{seq_id} || die,
-        $f->{start}-1, #< to zero-based
-        $f->{end}+0
-        );
-
-    return \@namerec;
+    if(exists $f->{seq_id}) {
+        my @namerec = (
+            \@names,
+            $self->{track_label},
+            $names[0],
+            $f->{seq_id},
+            $f->{start}-1, #< to zero-based
+            $f->{end}+0
+            );
+        return \@namerec;
+    }
+    else {
+        die;
+    }
 }
 sub arrayReprClasses {
     my ( $self ) = @_;