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[ADAM-1352] Clean up consensus model usage. #1357

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merged 1 commit into from Jan 19, 2017

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fnothaft commented Jan 19, 2017

Resolves #1352:

  • Fixed issues with consensus model instantiation.
  • Added union consensus model (to support multiple models).
  • Cleaned up consensus model documentation.
  • Call distinct in IndelRealigner on consensus sequences to eliminate dupes.
  • Added test for known indel model. Fixed off by one bug.
  • Add test for union model.

@fnothaft fnothaft added this to the 0.21.1 milestone Jan 19, 2017

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1742/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /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 -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/1357/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 1243c923d1edf86a2a436e3aa1369546180955d7 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1357/merge^{commit} # timeout=10Checking out Revision 1243c923d1edf86a2a436e3aa1369546180955d7 (origin/pr/1357/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 1243c923d1edf86a2a436e3aa1369546180955d7First 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.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1742/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /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 -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/1357/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 1243c923d1edf86a2a436e3aa1369546180955d7 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1357/merge^{commit} # timeout=10Checking out Revision 1243c923d1edf86a2a436e3aa1369546180955d7 (origin/pr/1357/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 1243c923d1edf86a2a436e3aa1369546180955d7First 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.

)
.fold(ConsensusGenerator.fromReads)(file => {
ConsensusGenerator.fromKnownIndels(rdd.rdd.context.loadVariants(file))
})

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heuermh Jan 19, 2017

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this reads a lot better

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heuermh Jan 19, 2017

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this reads a lot better

@@ -76,11 +64,12 @@ private[adam] object IndelTable {
val deletionLength = v.getReferenceAllele.length - v.getAlternateAllele.length
val start = v.getStart + v.getAlternateAllele.length
Consensus("", ReferenceRegion(referenceName, start, start + deletionLength))
Consensus("", ReferenceRegion(referenceName, start, start + deletionLength + 1))

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heuermh Jan 19, 2017

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oops :) was this a bug, or something you found when cleaning up? nm, saw it in the commit message

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heuermh Jan 19, 2017

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oops :) was this a bug, or something you found when cleaning up? nm, saw it in the commit message

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@fnothaft

fnothaft Jan 19, 2017

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This was a bug.

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fnothaft Jan 19, 2017

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This was a bug.

[ADAM-1352] Clean up consensus model usage.
Resolves #1352:

* Fixed issues with consensus model instantiation.
* Added union consensus model (to support multiple models).
* Cleaned up consensus model documentation.
* Call distinct in IndelRealigner on consensus sequences to eliminate dupes.
* Added test for known indel model. Fixed off by one bug.
* Add test for union model.
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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1743/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1743/
Test PASSed.

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This is good to go now.

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fnothaft commented Jan 19, 2017

This is good to go now.

@heuermh heuermh merged commit 9d7b4a3 into bigdatagenomics:master Jan 19, 2017

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Thank you, @fnothaft!

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heuermh commented Jan 19, 2017

Thank you, @fnothaft!

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