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

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merged 1 commit into from Mar 1, 2018
Merged

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

merged 1 commit into from Mar 1, 2018

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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 •
edited

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.
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heuermh requested changes Feb 9, 2018
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adam-python/bdgenomics/adam/rdd.py Outdated
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

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
Frank Austin Nothaft
[ADAM-1806] Add toVariants conversion from GenotypeRDD.
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3a1b677 
Resolves #1806.
@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
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@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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