two bugs fixed: coverage regions of level 2 and above were skipped. coverage...

two bugs fixed: coverage regions of level 2 and above were skipped. coverage regions of 2bp and less caused the problems for web display

modules/Bio/EnsEMBL/StrainSlice.pm

@@ -177,7 +177,7 @@ sub _filter_af_by_coverage{
     
     my $rc_adaptor = $variation_db->get_ReadCoverageAdaptor();
     #this is ugly, but ReadCoverage is always defined in the positive strand
-    my $rcs = $rc_adaptor->fetch_all_by_Slice_Sample_depth($self,$self->{'_strain'},1);
+    my $rcs = $rc_adaptor->fetch_all_by_Slice_Sample_depth($self,$self->{'_strain'});
     my $new_af;
     foreach my $af (@{$allele_features}){
 	foreach my $rc (@{$rcs}){
@@ -299,7 +299,7 @@ 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 = $rc_adaptor->fetch_all_by_Slice_Sample_depth($self,$self->{'_strain'});
     my $rcs_sorted;
     @{$rcs_sorted} = sort {$a->start <=> $b->start} @{$rcs} if ($self->strand == -1);
     $rcs = $rcs_sorted if ($self->strand == -1);
@@ -307,8 +307,8 @@ sub _add_coverage_information{
     foreach my $rc (@{$rcs}){
 	$rc->start(1) if ($rc->start < 0); #if the region lies outside the boundaries of the slice
 	$rc->end($self->end - $self->start + 1) if ($rc->end + $self->start > $self->end); 
-	substr($$reference_sequence, $start,($rc->start - $start - 1),'~' x ($rc->start - $start - 1)) if ($rc->start - 1 > $start); 
-	$start = $rc->end - 1;
+	substr($$reference_sequence, $start-1,($rc->start - $start - 1),'~' x ($rc->start - $start - 1)) if ($rc->start - 1 > $start);
+	$start = $rc->end ;
     }
     substr($$reference_sequence, $start, ($self->length - $start) ,'~' x ($self->length - $start)) if ($self->length -1 > $start); 
 }