modified to add proper coverage for negative strand

modules/Bio/EnsEMBL/StrainSlice.pm

@@ -273,6 +273,10 @@ sub _add_coverage_information{
     
     my $rc_adaptor = $variation_db->get_ReadCoverageAdaptor();
     my $rcs = $rc_adaptor->fetch_all_by_Slice_Sample_depth($self,$self->{'_strain'},1);
+    my $rcs_sorted;
+    @{$rcs_sorted} = sort {$a->start <=> $b->start} @{$rcs} if ($self->strand == -1);
+    $rcs = $rcs_sorted if ($self->strand == -1);
+    $$reference_sequence = reverse($$reference_sequence) if ($self->strand == -1);
     my $start = 0;
     foreach my $rc (@{$rcs}){
 	$rc->start(1) if ($rc->start < 0); #if the region lies outside the boundaries of the slice
@@ -281,6 +285,7 @@ sub _add_coverage_information{
 	$start = $rc->end - 1;
     }
     substr($$reference_sequence, $start, ($self->length - $start) ,'~' x ($self->length - $start)) if ($self->length -1 > $start); 
+    $$reference_sequence = reverse($$reference_sequence) if ($self->strand == -1);
 }