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

Updated GenomicPartitioners to accept additional key. #1147

Merged
merged 1 commit into from Sep 7, 2016

Conversation

Projects
None yet
4 participants
@akmorrow13
Contributor

akmorrow13 commented Sep 2, 2016

GenomicRegionPartitioner and GenomicPositionPartitioner can now accept an extra key. This can be used for keyBy() on cell type, sampleId, etc.

Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala
@@ -89,6 +89,16 @@ case class GenomicPositionPartitioner(numParts: Int, seqLengths: Map[String, Lon
)
getPart(refpos.referenceName, refpos.pos)
}
case (refpos: ReferencePosition, k: Any) => {
require(

This comment has been minimized.

@akmorrow13

akmorrow13 Sep 2, 2016

Contributor

There has got to be a cleaner way to do this. How can I piggyback these cases?
case (refpos: ReferencePosition) | (refpos: ReferencePosition, k: Any) throws an error because refpos cannot be defined twice...

@akmorrow13

akmorrow13 Sep 2, 2016

Contributor

There has got to be a cleaner way to do this. How can I piggyback these cases?
case (refpos: ReferencePosition) | (refpos: ReferencePosition, k: Any) throws an error because refpos cannot be defined twice...

This comment has been minimized.

@fnothaft

fnothaft Sep 2, 2016

Member

I think having them as separate cases is OK. I might pull the require(...) into the getPart, but this doesn't "smell" too bad to me.

@fnothaft

fnothaft Sep 2, 2016

Member

I think having them as separate cases is OK. I might pull the require(...) into the getPart, but this doesn't "smell" too bad to me.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Sep 2, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1453/
Test PASSed.

AmplabJenkins commented Sep 2, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1453/
Test PASSed.

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Sep 2, 2016

Member

LGTM, other than the nit RE: pulling things out into the helper function. I'm excited to have this in, @akmorrow13!

Member

fnothaft commented Sep 2, 2016

LGTM, other than the nit RE: pulling things out into the helper function. I'm excited to have this in, @akmorrow13!

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Sep 6, 2016

Member

+1

Member

heuermh commented Sep 6, 2016

+1

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Sep 7, 2016

Member

@akmorrow13 do you have the time to make the update that I referred to above, or would you prefer that I take that update on?

Member

fnothaft commented Sep 7, 2016

@akmorrow13 do you have the time to make the update that I referred to above, or would you prefer that I take that update on?

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Sep 7, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1462/

Build result: FAILURE

GitHub pull request #1147 of commit 0b9544b automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true 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/1147/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains e923b49ffb85c08bd2024b5d11bcf472a6d8b030 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1147/merge^{commit} # timeout=10Checking out Revision e923b49ffb85c08bd2024b5d11bcf472a6d8b030 (origin/pr/1147/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f e923b49ffb85c08bd2024b5d11bcf472a6d8b030First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Sep 7, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1462/

Build result: FAILURE

GitHub pull request #1147 of commit 0b9544b automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true 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/1147/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains e923b49ffb85c08bd2024b5d11bcf472a6d8b030 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1147/merge^{commit} # timeout=10Checking out Revision e923b49ffb85c08bd2024b5d11bcf472a6d8b030 (origin/pr/1147/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f e923b49ffb85c08bd2024b5d11bcf472a6d8b030First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Sep 7, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1463/

Build result: FAILURE

GitHub pull request #1147 of commit bb87a98 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true 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/1147/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains d0577d3cff8ca4199723b421b3cb46a2f0ed67e4 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1147/merge^{commit} # timeout=10Checking out Revision d0577d3cff8ca4199723b421b3cb46a2f0ed67e4 (origin/pr/1147/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d0577d3cff8ca4199723b421b3cb46a2f0ed67e4First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Sep 7, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1463/

Build result: FAILURE

GitHub pull request #1147 of commit bb87a98 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true 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/1147/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains d0577d3cff8ca4199723b421b3cb46a2f0ed67e4 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1147/merge^{commit} # timeout=10Checking out Revision d0577d3cff8ca4199723b421b3cb46a2f0ed67e4 (origin/pr/1147/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d0577d3cff8ca4199723b421b3cb46a2f0ed67e4First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Sep 7, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1464/
Test PASSed.

AmplabJenkins commented Sep 7, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1464/
Test PASSed.

@fnothaft fnothaft merged commit c728ea0 into bigdatagenomics:master Sep 7, 2016

1 check passed

default Merged build finished.
Details
@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Sep 7, 2016

Member

Merged! Thanks @akmorrow13!

Member

fnothaft commented Sep 7, 2016

Merged! Thanks @akmorrow13!

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