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Expose the ability to encode a Genotoype into a GT field #1648

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merged 2 commits into from
Jan 31, 2023

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lbergelson
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@droazen droazen left a comment

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One comment to address, otherwise looks good 👍


Assert.assertEquals(VCFEncoder.encodeGtField(vc, g1), "0/0");
Assert.assertEquals(VCFEncoder.encodeGtField(vc, g2), "1/2");
}
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Can you add a unit test for writeGtField() as well?

* Expose two public methods in VCFEncoder writeGtField and encodeGtField
* Supports broadinstitute/gatk#8160 but seems like a useful thing to be able to do in general
* minor breaking change in VCFEncoder, made methods formatVCFField and buildAlleleStrings static
  It is unlikely anyone overrides either of these methods so it should not be a problem.
@lbergelson lbergelson force-pushed the lb_expose_gt_encoding branch from 6f5230f to 0e6e942 Compare January 30, 2023 21:18
@lbergelson lbergelson merged commit 8108d56 into master Jan 31, 2023
@lbergelson lbergelson deleted the lb_expose_gt_encoding branch January 31, 2023 15:44
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2 participants