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More refactoring PDHCE and preparing for joint detection #8492

Merged
merged 21 commits into from
Sep 21, 2023
Merged

More refactoring PDHCE and preparing for joint detection #8492

merged 21 commits into from
Sep 21, 2023

Commits on Sep 20, 2023

  1. two very minor changes to AssemblyResultSet for conciseness

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    davidbenjamin committed Sep 20, 2023
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  2. added stream method to SmallBitSet

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    davidbenjamin committed Sep 20, 2023
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  3. assorted renaming

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  4. streamlining EventGroup code

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    davidbenjamin committed Sep 20, 2023
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  5. javadoc for nested loops

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    davidbenjamin committed Sep 20, 2023
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  6. PartiallyDeterminedHaplotype can handle multiple determined events

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    davidbenjamin committed Sep 20, 2023
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  7. initialize output haplotypes in one line

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    davidbenjamin committed Sep 20, 2023
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  8. eliminated the redundant variable determinedEventToTest

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    davidbenjamin committed Sep 20, 2023
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  9. Branching in terms of included events, not excluded events

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    davidbenjamin committed Sep 20, 2023
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  10. cleanup

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    davidbenjamin committed Sep 20, 2023
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  11. rename cachedExtent to determinedExtent

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  12. improved some doc text for nested loops

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  13. rename haplotypeEvenyts to fullyDeterminedHaplotypes

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    davidbenjamin committed Sep 20, 2023
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  14. more javadoc

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  15. unit test for event group clustering

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    davidbenjamin committed Sep 20, 2023
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  16. starting on unit tests for branching code

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  17. not exactly a bug fix as it doesn't affect output, but it makes branc… 

    …hing more correct
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  18. likewise, a change that doesn't affect output but internally enables … 

    …overlapping SNPs in PD haplotypes
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    davidbenjamin committed Sep 20, 2023
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  19. more branchign unit tests

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  20. whoops

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  21. commit?

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    davidbenjamin committed Sep 20, 2023
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