fixed bug in load_and_merge() when using --cache_method=build_cache_all

modules/Bio/EnsEMBL/IdMapping/Cache.pm

@@ -155,6 +155,9 @@ sub build_cache_by_slice {
   # write cache to file, then flush cache to reclaim memory
   my $size = $self->write_all_to_file($type);
 
+  # set cache method (required for loading cache later)
+  $self->cache_method('BY_SEQ_REGION');
+
   return $num_genes, $size;
 }
 
@@ -199,6 +202,9 @@ sub build_cache_all {
   # write cache to file, then flush cache to reclaim memory
   my $size = $self->write_all_to_file($type);
 
+  # set cache method (required for loading cache later)
+  $self->cache_method('ALL');
+
   return $num_genes, $size;
 }
 
@@ -1052,8 +1058,16 @@ sub read_and_merge {
     throw("Db type must be 'source' or 'target'.");
   }
 
-  foreach my $slice_name (@{ $self->slice_names($dbtype) }) {
-    $self->read_from_file("$dbtype.$slice_name");
+  # read cache from single or multiple files, depending on caching strategy
+  my $cache_method = $self->cache_method;
+  if ($cache_method eq 'ALL') {
+    $self->read_from_file("$dbtype.ALL");
+  } elsif ($cache_method eq 'BY_SEQ_REGION') {
+    foreach my $slice_name (@{ $self->slice_names($dbtype) }) {
+      $self->read_from_file("$dbtype.$slice_name");
+    }
+  } else {
+    throw("Unknown cache method: $cache_method.");
   }
 
   $self->merge($dbtype);
@@ -1196,6 +1210,13 @@ sub conf {
 }
 
 
+sub cache_method {
+  my $self = shift;
+  $self->{'instance'}->{'cache_method'} = shift if (@_);
+  return $self->{'instance'}->{'cache_method'};
+}
+
+
 sub highest_common_cs {
   my $self = shift;
   $self->{'instance'}->{'hccs'} = shift if (@_);