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[vds/combiner] use get_lgt for PGT handling as well #13829

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merged 2 commits into from Oct 17, 2023
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[vds/combiner] use get_lgt for PGT handling as well #13829

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[vds/combiner] use get_lgt for PGT handling as well
chrisvittal Oct 16, 2023
a32ed9c
need to unphase to get the index
chrisvittal Oct 16, 2023
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17 changes: 9 additions & 8 deletions hail/python/hail/vds/combiner/combine.py
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Expand Up @@ -30,16 +30,16 @@ def make_variants_matrix_table(mt: MatrixTable,

transform_row = _transform_variant_function_map.get((mt.row.dtype, info_key))
if transform_row is None or not hl.current_backend()._is_registered_ir_function_name(transform_row._name):
def get_lgt(e, n_alleles, has_non_ref, row):
index = e.GT.unphased_diploid_gt_index()
def get_lgt(gt, n_alleles, has_non_ref, row):
index = gt.unphased_diploid_gt_index()
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Is this function valid on phased GTs? Do we need to unphase it first?

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we do thanks for checking

n_no_nonref = n_alleles - hl.int(has_non_ref)
triangle_without_nonref = hl.triangle(n_no_nonref)
return (hl.case()
.when(e.GT.is_haploid(),
hl.or_missing(e.GT[0] < n_no_nonref, e.GT))
.when(index < triangle_without_nonref, e.GT)
.when(gt.is_haploid(),
hl.or_missing(gt[0] < n_no_nonref, gt))
.when(index < triangle_without_nonref, gt)
.when(index < hl.triangle(n_alleles), hl.missing('call'))
.or_error('invalid GT ' + hl.str(e.GT) + ' at site ' + hl.str(row.locus)))
.or_error('invalid GT ' + hl.str(gt) + ' at site ' + hl.str(row.locus)))

def make_entry_struct(e, alleles_len, has_non_ref, row):
handled_fields = dict()
Expand All @@ -53,11 +53,12 @@ def make_entry_struct(e, alleles_len, has_non_ref, row):
raise hl.utils.FatalError("the Hail VDS combiner expects input GVCFs to have a 'GT' field in FORMAT.")

handled_fields['LA'] = hl.range(0, alleles_len - hl.if_else(has_non_ref, 1, 0))
handled_fields['LGT'] = get_lgt(e, alleles_len, has_non_ref, row)
handled_fields['LGT'] = get_lgt(e.GT, alleles_len, has_non_ref, row)
if 'AD' in e:
handled_fields['LAD'] = hl.if_else(has_non_ref, e.AD[:-1], e.AD)
if 'PGT' in e:
handled_fields['LPGT'] = e.PGT
handled_fields['LPGT'] = e.PGT if e.PGT.dtype != hl.tcall \
else get_lgt(e.PGT, alleles_len, has_non_ref, row)
if 'PL' in e:
handled_fields['LPL'] = hl.if_else(has_non_ref,
hl.if_else(alleles_len > 2,
Expand Down