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densify_sites update #279

Merged
merged 5 commits into from
Jan 11, 2021
Merged

densify_sites update #279

merged 5 commits into from
Jan 11, 2021

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ch-kr
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@ch-kr ch-kr commented Jan 11, 2021

Sparse MTs were previously only keyed by locus by default. They are now keyed by locus and alleles by default

@ch-kr ch-kr requested a review from jkgoodrich January 11, 2021 17:41
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jkgoodrich reviewed Jan 11, 2021
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Should we make it an option with default False incase using an older MT?

@ch-kr ch-kr requested a review from jkgoodrich January 11, 2021 17:44
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Will both now be keyed by locus and alleles? will this always work?
last_END_positions_ht[sites_ht.key].last_END_position
what if sites_ht has different alleles but you still want to keep the locus?

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ch-kr commented Jan 11, 2021

that's a good point. what if I change compute_last_ref_block_end instead to always key by locus?

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Yeah both would need to be re_keyed by locus, so I think that will work

@ch-kr ch-kr requested a review from jkgoodrich January 11, 2021 17:58
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LGTM

@jkgoodrich jkgoodrich merged commit 2577ef4 into master Jan 11, 2021
@jkgoodrich jkgoodrich deleted the densify_sites branch January 11, 2021 18:07
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@ch-kr @jkgoodrich