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Allow custom ploidy regions in HaplotypeCaller #8464

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wants to merge 8 commits into from
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Allow custom ploidy regions in HaplotypeCaller #8464

wants to merge 8 commits into from

Commits on Nov 29, 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
    @rickymagner
    Ty Kay authored and rickymagner committed Nov 29, 2023
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Commits on Dec 1, 2023

  1. Add some tests and small tweaks

    @rickymagner
    rickymagner committed Dec 1, 2023
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Commits on Dec 7, 2023

  1. 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 7, 2023
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  2. woops.... (#8605) 

    * fix npe

* update comment and re-enable test
    @lbergelson
    lbergelson committed Dec 7, 2023
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  3. Update copy method and test

    @rickymagner
    rickymagner committed Dec 7, 2023
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  4. Remove old fields from HCE

    @rickymagner
    rickymagner committed Dec 7, 2023
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  5. Change data source to FeatureInput

    @rickymagner
    rickymagner committed Dec 7, 2023
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Commits on Dec 8, 2023

  1. Remove old commented code; add test arg copy sync deeper fields

    @rickymagner
    rickymagner committed Dec 8, 2023
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