AlignSlice can print sequences with different length, adding - when no base present

modules/Bio/EnsEMBL/AlignStrainSlice.pm

@@ -302,7 +302,33 @@ sub get_all_Slices {
   undef $ref_strain->{'alleleFeatures'};
   
   push @strains, @{$self->strains};
+  my $new_feature;
+  my $indel;
+  my $aligned_features;
+  my $indels = (); #reference to a hash containing indels in the different strains
+  #we need to realign all Features in the different Slices and add '-' in the reference Slice
+  foreach my $strain (@{$self->strains}){
+      foreach my $af (@{$strain->get_all_AlleleFeatures_Slice()}){
+	  $new_feature = $self->alignFeature($af); #align feature in AlignSlice coordinates
+	  push @{$aligned_features},$new_feature if($new_feature->seq_region_start <= $strain->end); #some features might map outside slice
+	  if ($af->start != $af->end){ #an indel, need to add to the reference, and realign in the strain	     
+              #make a shallow copy of the indel
+	      %{$indel} = %{$new_feature};
+	      bless $indel, ref($new_feature);
+	      $indel->allele_string('-');
+	      push @{$indels},$indel; #and include in the list of potential indels
+	  }
+      }
+      undef $strain->{'alleleFeatures'}; #remove all features before adding new aligned features
+      push @{$strain->{'alleleFeatures'}}, @{$aligned_features};
+      undef $aligned_features;
+  }  
   push @strains, $ref_strain;
+  #need to add indels in the different strains, if not present
+  foreach my $strain (@strains){
+      #inlcude the indels in the StrainSlice object
+      push @{$strain->{'alignIndels'}},@{$indels};
+  }
   return \@strains;
 }
 

modules/Bio/EnsEMBL/StrainSlice.pm

@@ -243,13 +243,20 @@ sub seq {
     my $seqAdaptor = $self->adaptor()->db()->get_SequenceAdaptor();
     my $reference_sequence = $seqAdaptor->fetch_by_Slice_start_end_strand($self,1,undef,1); #get the reference sequence for that slice
     #apply all differences to the reference sequence
+    #first, in case there are any indels, create the new sequence (containing the '-' bases)
+   # sort edits in reverse order to remove complication of
+    # adjusting downstream edits
+    my @indels_ordered = sort {$b->start() <=> $a->start()} @{$self->{'alignIndels'}} if (defined $self->{'alignIndels'});
 
+    foreach my $vf (@indels_ordered){
+	$vf->apply_edit($reference_sequence); #change, in the reference sequence, the vf
+    }
+    #need to find coverage information if diffe
     # sort edits in reverse order to remove complication of
     # adjusting downstream edits
     my @variation_features_ordered = sort {$b->start() <=> $a->start()} @{$self->{'alleleFeatures'}} if (defined $self->{'alleleFeatures'});
 
     foreach my $vf (@variation_features_ordered){
-	next if ($vf->start != $vf->end); #quick fix to remove indels from sequence
 	$vf->apply_edit($reference_sequence); #change, in the reference sequence, the vf
     }
     #need to find coverage information if different from reference