New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Merged
merged 1 commit into from Jul 25, 2017

Conversation

Projects
5 participants
@fnothaft
Member

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

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Jul 24, 2017

Member

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

Member

fnothaft commented Jul 24, 2017

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

@coveralls

This comment has been minimized.

Show comment
Hide comment
@coveralls

coveralls 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.

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.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins 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.

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.

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Jul 24, 2017

Member

Jenkins, retest this please.

Member

fnothaft commented Jul 24, 2017

Jenkins, retest this please.

@coveralls

This comment has been minimized.

Show comment
Hide comment
@coveralls

coveralls 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.

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.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins 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.

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.

@devin-petersohn

Looks good to me, one minor spacing question.

Show outdated Hide outdated adam-python/src/bdgenomics/adam/rdd.py Outdated
[ADAM-1614] Add VariantContextRDD to R and Python APIs.
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

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Jul 24, 2017

Member

Addressed comment.

Member

fnothaft commented Jul 24, 2017

Addressed comment.

@coveralls

This comment has been minimized.

Show comment
Hide comment
@coveralls

coveralls 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.

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.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins 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.

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,

This comment has been minimized.

@heuermh

heuermh Jul 25, 2017

Member

+1

@heuermh

heuermh Jul 25, 2017

Member

+1

@heuermh heuermh merged commit 7449b14 into bigdatagenomics:master Jul 25, 2017

3 checks passed

codacy/pr Good work! A positive pull request.
Details
coverage/coveralls Coverage remained the same at 83.961%
Details
default Merged build finished.
Details
@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Jul 25, 2017

Member

Thank you, @fnothaft

Member

heuermh commented Jul 25, 2017

Thank you, @fnothaft

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment