[vds] Add support for VDSes with truncated reference blocks #12645
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…s in filter_intervals
* add `hl.vds.truncate_reference_blocks` * add `hl.vds.merge_reference_blocks`
chrisvittal
previously requested changes
Feb 3, 2023
hail/python/hail/vds/methods.py
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| Notes | ||
| ----- | ||
| After this function has been run, the |
chrisvittal
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Feb 3, 2023
hail/python/hail/vds/methods.py
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| if ref_allele_function is None: | ||
| rg = ht.locus.dtype.reference_genome | ||
| if 'ref_allele' in ht.row: | ||
| ref_allele_function = lambda ht: ht.ref_allele |
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either ignore lint or use a def
hail/python/hail/vds/methods.py
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| if 'ref_allele' in ht.row: | ||
| ref_allele_function = lambda ht: ht.ref_allele | ||
| elif rg.has_sequence(): | ||
| ref_allele_function = lambda ht: ht.locus.sequence_context() |
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either ignore lint or use a def
hail/python/hail/vds/methods.py
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| ht = ht.annotate(prev_block=hl.zip(hl.scan.array_agg(lambda elt: hl.scan.fold((hl.null(rd.entry.dtype), False), | ||
| lambda acc: keep_last(acc, ( | ||
| elt, False)), | ||
| keep_last), ht.entries), ht.entries) |
| all_ref_max = n_with_ref_max_len == len(mts) | ||
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| # if some mts have max ref len but not all, drop it | ||
| new_ref_block_len_max = None |
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chrisvittal
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Feb 3, 2023
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CHANGELOG: introduce
hl.vds.truncate_reference_blocksto permit faster point queries against Hail VariantDatasets. Removeref_alleleas a required field in reference data.hl.vds.truncate_reference_blockshl.vds.merge_reference_blockshl.vds.filter_intervalsto use this