fix?

hail/python/hail/vds/methods.py

@@ -983,7 +983,7 @@ def truncate_reference_blocks(ds, *, max_ref_block_base_pairs=None, ref_block_wi
 
  # we've changed LEN so we need to make sure that END is correct.
  if 'END' in new_rd.entry:
- new_rd = VariantDataset._add_end(new_rd.drop('END'))
+ new_rd = new_rd.annotate_entries(END=new_rd.LEN + new_rd.locus.position - 1)
 
  if isinstance(ds, hl.vds.VariantDataset):
  return VariantDataset(reference_data=new_rd, variant_data=ds.variant_data)

hail/python/test/hail/vds/test_vds.py

@@ -895,11 +895,12 @@ def test_ref_block_does_not_densify_to_next_contig():
  ref = vds.reference_data
  var = vds.variant_data.filter_entries(False)
  # max out all chr1 refblocks, and truncate all chr2 refblocks so that nothing in chr2 should be densified
+ chr1_end = hl.parse_locus_interval('chr1', reference_genome=ref.locus.dtype.reference_genome).end.position
  ref = ref.annotate_entries(
- END=hl.if_else(
+ LEN=hl.if_else(
  ref.locus.contig == 'chr1',
- hl.parse_locus_interval('chr1', reference_genome=ref.locus.dtype.reference_genome).end.position,
- ref.locus.position,
+ chr1_end - ref.locus.position + 1,
+ 1,
  )
  )
  vds = hl.vds.VariantDataset(reference_data=ref, variant_data=var)