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[ADAM-1806] Add toVariants conversion from GenotypeRDD. #1904

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@fnothaft fnothaft commented Feb 5, 2018

Resolves #1806.

@fnothaft fnothaft added this to the 0.24.0 milestone Feb 5, 2018
@fnothaft fnothaft requested a review from heuermh Feb 5, 2018
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@fnothaft fnothaft commented Feb 5, 2018

Just realized, this needs to propagate through to R/Python as well.

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@heuermh heuermh commented Feb 5, 2018

Just realized, this needs to propagate through to R/Python as well.

Yep, at least we haven't spread ourselves too thin. ;)

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@coveralls coveralls commented Feb 5, 2018

Coverage Status

Coverage decreased (-0.03%) to 82.53% when pulling dc6f761 on fnothaft:issues/1806-genotypes-to-variants into aa43a56 on bigdatagenomics:master.

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@coveralls coveralls commented Feb 5, 2018

Coverage Status

Coverage decreased (-0.03%) to 82.53% when pulling dc6f761 on fnothaft:issues/1806-genotypes-to-variants into aa43a56 on bigdatagenomics:master.

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@coveralls coveralls commented Feb 5, 2018

Coverage Status

Coverage decreased (-0.03%) to 82.53% when pulling dc6f761 on fnothaft:issues/1806-genotypes-to-variants into aa43a56 on bigdatagenomics:master.

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@coveralls coveralls commented Feb 5, 2018

Coverage Status

Coverage increased (+0.1%) to 82.691% when pulling 3a1b677 on fnothaft:issues/1806-genotypes-to-variants into c691356 on bigdatagenomics:master.

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@AmplabJenkins AmplabJenkins commented Feb 5, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2644/
Test PASSed.

@fnothaft fnothaft force-pushed the fnothaft:issues/1806-genotypes-to-variants branch from dc6f761 to 40beacf Feb 9, 2018
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@fnothaft fnothaft commented Feb 9, 2018

This is good to go from my side now.

Does not perform any filtering looking at whether the variant was called
or not. By default, does not deduplicate variants. By default, does not
deduplicate variants.

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Doc comment needs deduplicating.

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fnothaft Feb 13, 2018
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Ironic!

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@AmplabJenkins AmplabJenkins commented Feb 9, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2658/
Test PASSed.

@heuermh heuermh added this to Triage in Release 0.24.0 Feb 10, 2018
@fnothaft fnothaft force-pushed the fnothaft:issues/1806-genotypes-to-variants branch from 40beacf to 3a1b677 Mar 1, 2018
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@fnothaft fnothaft commented Mar 1, 2018

Addressed reviewer comments.

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@AmplabJenkins AmplabJenkins commented Mar 1, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2686/
Test PASSed.

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heuermh approved these changes Mar 1, 2018
@heuermh heuermh merged commit 7761e6e into bigdatagenomics:master Mar 1, 2018
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Codacy/PR Quality Review Good work! A positive pull request.
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@heuermh heuermh commented Mar 1, 2018

Thank you, @fnothaft

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