Non-extended summary retrieval for BigWigs.

Created by: ens-ds23

Saves us having to do the computation ourselves.

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

@@ -77,7 +77,7 @@ sub munge_chr_id {
   return $ret_id;
 }
 
-sub fetch_extended_summary_array {
+sub fetch_summary_array {
   my ($self, $chr_id, $start, $end, $bins, $has_chrs) = @_;
 
   my $bw = $self->bigwig_open;
@@ -88,6 +88,28 @@ sub fetch_extended_summary_array {
   my $seq_id = $has_chrs ? $self->munge_chr_id($chr_id) : $chr_id;
   return [] if !defined($seq_id);
 
+# Remember this method takes half-open coords (subtract 1 from start)
+  my $summary = $bw->bigWigSummaryArray("$seq_id",$start-1,$end,0,$bins);
+
+  if ($DEBUG) {
+    warn " *** fetch extended summary: $chr_id:$start-$end : found ", scalar(@$summary), " summary points\n";
+  }
+
+  return $summary;
+}
+
+
+sub fetch_extended_summary_array {
+  my ($self, $chr_id, $start, $end, $bins, $has_chrs) = @_;
+
+  my $bw = $self->bigwig_open;
+  warn "Failed to open BigWig file" . $self->url unless $bw;
+  return [] unless $bw;
+
+  #  Maybe need to add 'chr' (only try if species has chromosomes)
+  my $seq_id = $has_chrs ? $self->munge_chr_id($chr_id) : $chr_id;
+  return [] if !defined($seq_id);
+
 # Remember this method takes half-open coords (subtract 1 from start)
   my $summary_e = $bw->bigWigSummaryArrayExtended("$seq_id",$start-1,$end,$bins);