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Passing implementation of custom ploidy regions in HaplotypeCaller #8609

Merged
merged 5 commits into from
Dec 11, 2023
Merged

Passing implementation of custom ploidy regions in HaplotypeCaller #8609

merged 5 commits into from
Dec 11, 2023

Commits on Dec 8, 2023

  1. creates multiple enginges to handle different ploidies 

    Finish changes to HaplotypeCaller to add ploidy-regions flag allowing variable ploidy

Change IntervalFileFeature interface to NamedFeature for htsjdk dependency

Address comments for draft PR

Make a few changes and refactors based on comments

Add some tests and small tweaks
    @lbergelson
    Ty Kay authored and lbergelson committed Dec 8, 2023
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  2. Extracted a cache of Genotypers indexed by ploidy (#8598) 

    * Introduced a new class MulitPloidyGenotyperCache which keeps track of multiple GenotypingEngines that have different ploidy values.  
* minor refactoring in related classes
* removed an unused type parameter from GenotypingEngine
    @lbergelson
    lbergelson committed Dec 8, 2023
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  3. Update copy method and test 

    Remove old fields from HCE

Change data source to FeatureInput

Remove old commented code; add test arg copy sync deeper fields
    @rickymagner @lbergelson
    rickymagner authored and lbergelson committed Dec 8, 2023
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  4. Revert "Extracted a cache of Genotypers indexed by ploidy (#8598)" 

    This reverts commit a40ba3e.
    @lbergelson
    lbergelson committed Dec 8, 2023
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  5. Update new test for copying arg sync

    @rickymagner
    rickymagner committed Dec 8, 2023
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