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[ADAM-1614] Add VariantContextRDD to R and Python APIs. #1628

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@fnothaft
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@fnothaft fnothaft commented Jul 24, 2017

Resolves #1614. Restructures both R and Python APIs to add GenomicDataset class, which inherits from GenomicRDD, as in adam-core. Moves all implementing classes onto GenomicDataset, and adds VariantContextRDD which is the lone class that extends GenomicRDD. Deletes saveAsVcf from GenotypeRDD and VariantRDD, and moves this functionality into toVariantContextRDD functions and VariantContextRDD.saveAsVcf. Additionally, adds sort and sortLexicographically to the R API, and fixes sortLexicographically in the Python API (it was calling sort previously).

@fnothaft fnothaft added this to the 0.23.0 milestone Jul 24, 2017
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@fnothaft fnothaft commented Jul 24, 2017

From a sequencing perspective, I think this change has fewer moving parts and should probably merge before #1627.

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@coveralls coveralls commented Jul 24, 2017

Coverage Status

Coverage remained the same at 83.961% when pulling 158fd57 on fnothaft:issues/1614-variantcontextrdd-r-python into 9bc5e15 on bigdatagenomics:master.

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@AmplabJenkins AmplabJenkins commented Jul 24, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2277/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1628/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 298babfc8347dc5365a02712d61e50e66947d40f # timeout=10Checking out Revision 298babfc8347dc5365a02712d61e50e66947d40f (origin/pr/1628/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 298babfc8347dc5365a02712d61e50e66947d40fFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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@fnothaft fnothaft commented Jul 24, 2017

Jenkins, retest this please.

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@coveralls coveralls commented Jul 24, 2017

Coverage Status

Coverage remained the same at 83.961% when pulling 158fd57 on fnothaft:issues/1614-variantcontextrdd-r-python into 9bc5e15 on bigdatagenomics:master.

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@AmplabJenkins AmplabJenkins commented Jul 24, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2278/
Test PASSed.

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@devin-petersohn devin-petersohn left a comment

Looks good to me, one minor spacing question.

"""

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Was this spacing addition intentional?

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@fnothaft

fnothaft Jul 24, 2017
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Nope, I'll clean that.

Resolves #1614. Restructures both R and Python APIs to add `GenomicDataset`
class, which inherits from `GenomicRDD`, as in adam-core. Moves all implementing
classes onto `GenomicDataset`, and adds `VariantContextRDD` which is the lone
class that extends `GenomicRDD`. Deletes `saveAsVcf` from `GenotypeRDD` and
`VariantRDD`, and moves this functionality into `toVariantContextRDD` functions
and `VariantContextRDD.saveAsVcf`. Additionally, adds `sort` and
`sortLexicographically` to the R API, and fixes `sortLexicographically` in
the Python API (it was calling `sort` previously).
@fnothaft fnothaft force-pushed the fnothaft:issues/1614-variantcontextrdd-r-python branch from 158fd57 to c6cf39f Jul 24, 2017
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@fnothaft fnothaft commented Jul 24, 2017

Addressed comment.

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@coveralls coveralls commented Jul 24, 2017

Coverage Status

Coverage remained the same at 83.961% when pulling c6cf39f on fnothaft:issues/1614-variantcontextrdd-r-python into 9bc5e15 on bigdatagenomics:master.

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@AmplabJenkins AmplabJenkins commented Jul 24, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2279/
Test PASSed.

genotypes.saveAsVcf(tmpPath,
asSingleFile=True,
sortOnSave=True)
genotypes.toVariantContextRDD().sort().saveAsVcf(tmpPath,

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@heuermh heuermh merged commit 7449b14 into bigdatagenomics:master Jul 25, 2017
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codacy/pr Good work! A positive pull request.
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coverage/coveralls Coverage remained the same at 83.961%
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default Merged build finished.
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@heuermh
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@heuermh heuermh commented Jul 25, 2017

Thank you, @fnothaft

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018
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