Fixes to handle strandedness of slices and requested sequences in the...

Fixes to handle strandedness of slices and requested sequences in the fetch_by_Slice_start_end_strand method.

modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm

@@ -142,15 +142,31 @@ sub fetch_by_Slice_start_end_strand {
      $end = $slice->chr_end() - $slice->chr_start() + 1;
    }
 
-   $self->fetch_by_assembly_location
-     (
-      $slice->chr_start()+$start-1,
-      $slice->chr_start()+$end-1,
-      $strand,
-      $slice->chr_name(),
-      $slice->assembly_type() 
-     );
-   
+   # need to check the strand'edness of the slice as this
+   # affects the direction in which the dna seq is grabbed
+   if ( $slice->strand == 1 ) {
+     $self->fetch_by_assembly_location
+       (
+	$slice->chr_start()+$start-1,
+	$slice->chr_start()+$end-1,
+	$strand,
+	$slice->chr_name(),
+	$slice->assembly_type() 
+       );
+   }
+   elsif ( $slice->strand == -1 ) {
+     $self->fetch_by_assembly_location
+       (
+	$slice->chr_end()-$end+1,
+	$slice->chr_end()-$start+1,
+	$strand,
+	$slice->chr_name(),
+	$slice->assembly_type() 
+       );
+   }
+   else {
+     self->throw("Incorrect strand set on slice $slice");
+   }
 }