do not return undef, just return

modules/Bio/EnsEMBL/IO/Adaptor/BAMAdaptor.pm

@@ -101,7 +101,7 @@ sub munge_chr_id {
 
   my $bam = $self->bam_open;
   warn "Failed to open BAM file " . $self->url unless $bam;
-  return undef unless $bam;
+  return unless $bam;
 
   my $header = $bam->header;
 
@@ -130,7 +130,7 @@ sub munge_chr_id {
   }
 
   warn " *** could not parse_region for BAM with $chr_id in file " . $self->url ."\n";
-  return undef;
+  return;
 }
 
 sub fetch_paired_alignments {

modules/Bio/EnsEMBL/IO/Adaptor/BigBedAdaptor.pm

@@ -130,7 +130,7 @@ sub munge_chr_id {
   
   warn "Failed to open BigBed file " . $self->url unless $bb;
   
-  return undef unless $bb;
+  return unless $bb;
 
   my $list = $bb->chromList;
   my $head = $list->head;

modules/Bio/EnsEMBL/IO/Adaptor/BigWigAdaptor.pm

@@ -77,7 +77,7 @@ sub munge_chr_id {
   
   warn "Failed to open BigWig file " . $self->url unless $bw;
   
-  return undef unless $bw;
+  return unless $bw;
 
   my $list = $bw->chromList;
   my $head = $list->head;

modules/Bio/EnsEMBL/IO/Adaptor/HTSAdaptor.pm

@@ -107,7 +107,7 @@ sub munge_chr_id {
   }
 
   warn " *** could not parse_region for BAM/CRAM with $chr_id in file " . $self->url ."\n";
-  return undef;
+  return;
 }
 
 sub fetch_paired_alignments {

modules/Bio/EnsEMBL/IO/ColumnBasedParser.pm

@@ -312,7 +312,7 @@ sub validate_metadata {
     ## TODO - implement validation! 
   }
 
-  return undef;
+  return;
 }
 
 =head2 validate_record

modules/Bio/EnsEMBL/IO/ListBasedParser.pm

@@ -57,9 +57,9 @@ sub open {
 
 ## This format has no metadata
 
-sub is_metadata { return undef; }
+sub is_metadata { return; }
 
-sub read_metadata { return undef; }
+sub read_metadata { return; }
 
 =head2 read_record
 

modules/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm

@@ -619,7 +619,7 @@ sub get_info_description {
 
 sub get_raw_formats {
   my $self = shift;
-  return undef if (!$self->get_metadata_by_pragma('header')->[8] || $self->get_metadata_by_pragma('header')->[8] ne 'FORMAT');
+  return if (!$self->get_metadata_by_pragma('header')->[8] || $self->get_metadata_by_pragma('header')->[8] ne 'FORMAT');
   return $self->{'record'}[8];
 }
 
@@ -667,14 +667,14 @@ sub get_metadata_description {
 
   if (!defined($type) || !defined($id)) {
     carp("You need to provide a meta type (e.g. 'INFO') and a meta entry ID (e.g. 'AA')");
-    return undef;
+    return;
   }
 
   my $meta = $self->get_metadata_by_pragma($type);
   foreach my $meta_entry (@$meta) {
     return $meta_entry->{'Description'} if ($meta_entry->{'ID'} eq $id);
   }
-  return undef;
+  return;
 }
 
 

modules/Bio/EnsEMBL/IO/Parser/Pileup.pm

@@ -60,9 +60,9 @@ sub open {
 
 ## This format has no metadata
 
-sub is_metadata { return undef; }
+sub is_metadata { return; }
 
-sub read_metadata { return undef; }
+sub read_metadata { return; }
 
 =head2 set_fields
 

modules/Bio/EnsEMBL/IO/Parser/VEP_input.pm

@@ -58,9 +58,9 @@ sub open {
 
 ## This format has no metadata
 
-sub is_metadata { return undef; }
+sub is_metadata { return; }
 
-sub read_metadata { return undef; }
+sub read_metadata { return; }
 
 =head2 set_fields
 

modules/Bio/EnsEMBL/IO/Parser/VEP_output.pm

@@ -62,7 +62,7 @@ sub is_metadata {
 
 sub read_metadata {
 ### No useful metadata, just column names
-  return undef;
+  return;
 }
 
 =head2 set_fields

modules/Bio/EnsEMBL/IO/Parser/Wig.pm

@@ -274,7 +274,7 @@ sub get_score {
   my $self = shift;
   my $val = $self->get_raw_score();
   if ($val && $val =~ /^\.$/) {
-    return undef;
+    return;
   } else {
     return $val;
   }

modules/Bio/EnsEMBL/IO/Translator.pm

@@ -168,7 +168,7 @@ sub get_field {
     }
 
     # If the field doesn't exist, return undef
-    return undef;
+    return;
 }
 
 =head2 batch_fields
@@ -230,7 +230,7 @@ sub fetch_callback {
     }
 
     # If the field doesn't exist, return undef
-    return undef
+    return;
 }
 
 1;

modules/Bio/EnsEMBL/IO/Translator/StructuralVariationFeature.pm

@@ -283,7 +283,7 @@ sub sv_cipos {
 
     return "$info=$cipos";
   } else {
-    return undef;
+    return;
   }
 }
 
@@ -300,7 +300,7 @@ sub sv_ciend {
 
     return "$info=$ciend";
   } else {
-    return undef;
+    return;
   }
 }
 
@@ -312,7 +312,7 @@ sub sv_imprecise {
   if (($object->outer_start && $object->inner_start) || ($object->inner_end && $object->outer_end)) {
     return $info;
   } else {
-    return undef;
+    return;
   }
 }
 

modules/EnsEMBL/Web/File/Utils.pm

@@ -50,7 +50,7 @@ sub sanitise_path {
       }
     }
     else {
-      return undef;
+      return;
     }
   }
 
@@ -127,7 +127,7 @@ sub get_compression {
     return 'gz'   if $file =~ /\.gz$/;
     return 'zip'  if $file =~ /\.zip$/;
     return 'bz'   if $file =~ /\.bz2?$/;
-    return undef;
+    return;
   }
 }
 

modules/EnsEMBL/Web/File/Utils/FileSystem.pm

@@ -43,7 +43,7 @@ sub create_path {
   my @directories   = make_path($path, { %$params, 'error' => \my $error });
 
   if (@$error) {
-    return undef if $no_exception;
+    return if $no_exception;
     throw(sprintf qq(Could not create the given path '%s' due to following errors: \n%s), $path, displayable_error($error));
   }
 
@@ -62,7 +62,7 @@ sub remove_directory {
   my $file_count    = remove_tree($path, { %$params, 'error' => \my $error});
 
   if (@$error) {
-    return undef if $no_exception;
+    return if $no_exception;
     throw(sprintf qq(Could not remove the given directory '%s' due to following errors: \n%s), $path, displayable_error($error));
   }
 
@@ -111,14 +111,14 @@ sub copy_dir_contents {
   my $no_exception  = delete $params->{'no_exception'};
   my $contents      = [];
   my %exclude       = map { $_ =~ s/\/$//r => 1 } @{$params->{'exclude'} || []};
-  my $dir_contents  = list_dir_contents($source_dir, {'no_exception' => $no_exception}) or return undef;
+  my $dir_contents  = list_dir_contents($source_dir, {'no_exception' => $no_exception}) or return;
 
   if (!-d $dest_dir) {
     if ($params->{'create_path'}) {
       push @$contents, @{ create_path($dest_dir) };
     } else {
       throw("Destination directory $dest_dir does not exist.") unless $no_exception;
-      return undef;
+      return;
     }
   }
 
@@ -188,7 +188,7 @@ sub list_dir_contents {
 
   if (!$dh) {
     throw("An error occurred while reading the directory $dir: $!") unless $params->{'no_exception'};
-    return undef;
+    return;
   }
 
   while (my $content = $dh->read) {

modules/EnsEMBL/Web/File/Utils/IO.pm

@@ -191,7 +191,7 @@ sub fetch_file {
   else {
     if ($@) {
       throw(sprintf qq(Could not fetch contents of file '%s' due to following errors: \n%s), $path, $@) unless $args->{'no_exception'};
-      return undef;
+      return;
     }
     else {
       return $content;
@@ -237,7 +237,7 @@ sub read_file {
   else {
     if ($@) {
       throw(sprintf qq(Could not read file '%s' due to following errors: \n%s), $path, $@) unless $args->{'no_exception'};
-      return undef;
+      return;
     }
     else {
       return $content;
@@ -285,7 +285,7 @@ sub read_lines {
   else {
     if ($@) {
       throw(sprintf qq(Could not read lines from file '%s' due to following errors: \n%s), $path, $@) unless $args->{'no_exception'};
-      return undef;
+      return;
     }
     else {
       return $content;
@@ -347,7 +347,7 @@ sub preview_file {
   else {
     if ($@) {
       throw(sprintf qq(Could not fetch preview of file '%s' due to following errors: \n%s), $path, $@) unless $args->{'no_exception'};
-      return undef;
+      return;
     }
     else {
       return $lines;