Fix for multiple assemblies breaks haplotype projection so removed

modules/Bio/EnsEMBL/Mapper.pm

@@ -223,10 +223,17 @@ sub map_coordinates{
      my $self_coord   = $pair->{$from};
      my $target_coord = $pair->{$to};
 
-     if($self_coord->{'start'} < $start){
-       $start = $orig_start;
-       $rank++;
-     }
+
+
+#
+# But not the case for haplotypes!! need to test for this case???
+# so removing this till a better solution is found
+#
+#
+#     if($self_coord->{'start'} < $start){
+#       $start = $orig_start;
+#       $rank++;
+#     }
 
 
      if(defined($last_target_coord) and $target_coord->{'id'} ne $last_target_coord){

modules/Bio/EnsEMBL/Slice.pm

@@ -808,10 +808,11 @@ sub project {
       my $coord_end    = $coord->end();
       my $length       = $coord_end - $coord_start + 1;
       
-      if( $last_rank != $coord->rank){
-	$current_start = 1;
-      }
-      $last_rank = $coord->rank;
+#      if( $last_rank != $coord->rank){
+#	$current_start = 1;
+#	print "LAST rank has changed to ".$coord->rank."from $last_rank \n";
+#     }
+#      $last_rank = $coord->rank;
 
       #skip gaps
       if($coord->isa('Bio::EnsEMBL::Mapper::Coordinate')) {