Code

Preserve VCF fields in MAF output#4872

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LeeTL1220 merged 7 commits intomasterbroadinstitute/gatk:masterfrom ll_VCF_MAF_field_preservationbroadinstitute/gatk:ll_VCF_MAF_field_preservationCopy head branch name to clipboardJun 15, 2018

+1,024-430

Commits

Commits on Jun 13, 2018

• Creating FuncotationMetadata for getting a catalog of fields before rendering. This is very useful for internal consistency.

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• Minor change to fix some rebase issues.

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• Removed AF from tumor_f, since it was coming from INFO instead of FORMAT.

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• Answering PR comments.

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Commits on Jun 14, 2018

• Several fixes discovered post-rebase onto master.

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Commits on Jun 15, 2018

• Adding workaround to address a unit test that was using test data that had "END" column which was throwing off MAF processing.

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• Fixed javadoc

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