Altering the feature iteration code to while and shift rather than foreaching...

Altering the feature iteration code to while and shift rather than foreaching the array. It's far more memory efficient as we are dumping data once we are finished with it

modules/Bio/EnsEMBL/Utils/SeqDumper.pm

@@ -724,7 +724,8 @@ sub _dump_feature_table {
   }
 
   foreach my $gene_slice (@gene_slices) {
-    foreach my $gene (@{$gene_slice->get_all_Genes(undef,undef, 1)}) {
+    my @genes = @{$gene_slice->get_all_Genes(undef,undef, 1)};
+    while(my $gene = shift @genes) {
       $value = $self->features2location( [$gene] );
       $self->write( @ff, 'gene', $value );
       $self->write( @ff, "", '/gene='.$gene->stable_id() );
@@ -800,7 +801,8 @@ sub _dump_feature_table {
   #
   if($self->is_enabled('genscan')) {
     my @genscan_exons;
-    foreach my $transcript(@{$slice->get_all_PredictionTranscripts(undef,1)}) {
+    my @transcripts = @{$slice->get_all_PredictionTranscripts(undef,1)};
+    while(my $transcript = shift @transcripts) {
       my $exons = $transcript->get_all_Exons();
       push @genscan_exons, @$exons;
       $self->write(@ff, 'mRNA', $self->features2location($exons));
@@ -818,7 +820,8 @@ sub _dump_feature_table {
   if($self->is_enabled('variation') && $slice->can('get_all_VariationFeatures')) {
 #    $slice->adaptor->db->add_db_adaptor('lite', $lite) if $lite;
 
-    foreach my $snp (@{$slice->get_all_VariationFeatures}) {
+    my @variations = @{$slice->get_all_VariationFeatures()};
+    while(my $snp = shift @variations) {
       my $ss = $snp->start;
       my $se = $snp->end;
       #skip snps that hang off edge of slice
@@ -854,9 +857,9 @@ sub _dump_feature_table {
   # repeats
   #
   if($self->is_enabled('repeat')) {
-    my $rfs = $slice->get_all_RepeatFeatures();
+    my @rfs = @{$slice->get_all_RepeatFeatures()};
 
-    foreach my $repeat (@$rfs) {
+    while(my $repeat = shift @rfs) {
       $self->write(@ff, 'repeat_region', $self->features2location([$repeat]));
       $self->write(@ff, ''    , '/note="' . $repeat->repeat_consensus->name.
 		   ' repeat: matches ' . $repeat->hstart.'..'.$repeat->hend .
@@ -869,7 +872,8 @@ sub _dump_feature_table {
   # markers
   #
   if($self->is_enabled('marker') && $slice->can('get_all_MarkerFeatures')) {
-    foreach my $mf (@{$slice->get_all_MarkerFeatures}) {
+    my @markers = @{$slice->get_all_MarkerFeatures()};
+    while(my $mf = shift @markers) {
       $self->write(@ff, 'STS', $self->features2location([$mf]));
       if($mf->marker->display_MarkerSynonym) {
         $self->write(@ff, ''   , '/standard_name="' .