[query] add hl.utils.genomic_range_table#12679
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danking merged 6 commits intohail-is:mainfrom Feb 16, 2023
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CHANGELOG: In Query on Batch, `hl.balding_nichols_model` is slightly faster. Also added `hl.utils.genomic_range_table` to quickly create a table keyed by locus. It has grated on me for a while that `hl.balding_nichols_models` requires a whole pass to verify it is sorted even though it is plainly so. This change introduces the necessary infrastructure to convince Hail of that fact.
chrisvittal
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Feb 10, 2023
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chrisvittal
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I have no major objections to this, but I am curious as to why you went the route of a new table IR, rather than implementing this with the unsafe key by on a normal range table?
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AFAIK, unsafe key-by would still do an unnecessary scan across the data to compute partition bounds. This IR is exactly 1 pass (instead of 2). |
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February 13, 2023 10:49
chrisvittal
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Feb 13, 2023
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CHANGELOG: In Query on Batch,
hl.balding_nichols_modelis slightly faster. Also addedhl.utils.genomic_range_tableto quickly create a table keyed by locus.It has grated on me for a while that
hl.balding_nichols_modelsrequires a whole pass to verify it is sorted even though it is plainly so. This change introduces the necessary infrastructure to convince Hail of that fact.