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rebase Dgs configure plugin packages #5573

Merged
merged 6 commits into from
Jan 23, 2019
Merged

rebase Dgs configure plugin packages #5573

merged 6 commits into from
Jan 23, 2019

Commits on Jan 23, 2019

  1. Add configuration option for ReadFilter plugin

    @magicDGS @lbergelson
    magicDGS authored and lbergelson committed Jan 23, 2019
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  2. Add configuration option for Annotation plugin

    @magicDGS @lbergelson
    magicDGS authored and lbergelson committed Jan 23, 2019
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  3. Use configuration in VariantAnnotatorEngine too

    @magicDGS @lbergelson
    magicDGS authored and lbergelson committed Jan 23, 2019
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  4. Rebasing and updating, adding tests. 

    * added tests to show that the Annotation /ReadFilter loading is
controlled by the config file
* added a new method to base test runToolInNewJvm which lets you run a
gatk tool in a clean jvm so you can alter static state like which config
file was used.

Co-authored-by: Louis Bergelson <louisb@broadinstitute.org>
    @lbergelson
    lbergelson committed Jan 23, 2019
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  5. remove accidentally included test

    @lbergelson
    lbergelson committed Jan 23, 2019
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  6. responding to comments

    @lbergelson
    lbergelson committed Jan 23, 2019
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