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Port LeftAlignAndTrimVariants from GATK3 #5144

Merged
merged 17 commits into from
Sep 14, 2018
Merged

Port LeftAlignAndTrimVariants from GATK3 #5144

merged 17 commits into from
Sep 14, 2018

Commits on Sep 14, 2018

  1. LeftAlignAndTrimVariants added

    @kachulis
    kachulis committed Sep 14, 2018
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  2. tests for LeftAlignAndTrimVariants

    @kachulis
    kachulis committed Sep 14, 2018
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  3. working on tests

    @kachulis
    kachulis committed Sep 14, 2018
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  4. LeftAlignAndTrimVariants tests

    @kachulis
    kachulis committed Sep 14, 2018
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  5. tests for LeftAlignAndTrimVariants

    @kachulis
    kachulis committed Sep 14, 2018
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  6. adding check to never left align to before the end of a previous variant

    @kachulis
    kachulis committed Sep 14, 2018
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  7. fix LeftAlignAndTrimVariantsIntegrationTest after rebase

    @kachulis
    kachulis committed Sep 14, 2018
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  8. aesthetic changes

    @kachulis
    kachulis committed Sep 14, 2018
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  9. if refLength longer than max_indel_length, still write out variant, j… 

    …ust don't try to left align
    @kachulis
    kachulis committed Sep 14, 2018
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  10. additional test case

    @kachulis
    kachulis committed Sep 14, 2018
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  11. soohee functionality requests

    @kachulis
    kachulis committed Sep 14, 2018
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  12. consolidating subsetAlleles code as requested by James

    @kachulis
    kachulis committed Sep 14, 2018
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  13. changes and additional tests requested by James

    @kachulis
    kachulis committed Sep 14, 2018
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  14. fixing example usage

    @kachulis
    kachulis committed Sep 14, 2018
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  15. fixing test failure in GATKVariantContextUtilsUnitTest

    @kachulis
    kachulis committed Sep 14, 2018
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  16. small aesthetic change

    @kachulis
    kachulis committed Sep 14, 2018
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  17. fixing merge conflict and removing unintended intelliJ reformatting

    @kachulis
    kachulis committed Sep 14, 2018
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