LA entry is "NA" when samples is hom-ref in VDS

Hail Query & hailctl
1

Hi, I’m a bit struggling with formatting my VDS file from local to global. Currently I have to following code to transform my local entries LAD and LGT into their global equivalent:

mt = vds.variant_data.annotate_entries(
  AD = hl.vds.local_to_global(vds.variant_data.LAD,
                              vds.variant_data.LA,
                              n_alleles=hl.len(vds.variant_data.alleles),
                              fill_value=0,
                              number="R")
)

# Transform local genotype to global
mt = mt.annotate_entries(GT = hl.vds.lgt_to_gt(mt.LGT, mt.LA))

# Densify to MT
mt = hl.vds.to_dense_mt(hl.vds.VariantDataset(vds.reference_data, mt))

The resulting mt has the following format:

+----------------+------------+------+-----------------------+------+-------+
| locus          | alleles    | rsid | s                     | GT   |    GQ |
+----------------+------------+------+-----------------------+------+-------+
| locus<GRCh38>  | array<str> | str  | str                   | call | int32 |
+----------------+------------+------+-----------------------+------+-------+
| chr1:100000    | ["G","T"]  | NA   | "SAMPLE"              | 0/0  |    81 |

| AD           |    DP | LGT  | LAD          | LA           |
+--------------+-------+------+--------------+--------------+
| array<int32> | int32 | call | array<int32> | array<int32> |
+--------------+-------+------+--------------+--------------+
| NA           |    41 | 0/0  | [41]         | NA           |

The issue I’m having is that LA is a NA when the sample is hom-ref, and therefore AD is NA as well. What would be the easiest way to fix it?

I’ve tried the following snippet, with no luck:

# Annotate AD: If it's missing, create a array of length two with LAD, and DP - LAD
mt=mt.annotate_entries(AD=hl.or_else(mt.AD,hl.array([mt.LAD[0],mt.DP-mt.LAD[0]])))

Thanks!