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Refactor Genotype and GenotypeAnnotation #2117

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commented Jan 16, 2019

Work in progress.
Companion pull request to bigdatagenomics/bdg-formats#176.

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commented Jan 16, 2019

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2937/

Build result: FAILURE

GitHub pull request #2117 of commit d2352e7 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-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2117/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 119bc88 # timeout=10Checking out Revision 119bc88 (origin/pr/2117/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 119bc886d21d353c073863b60c85afa9dcb0312fFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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commented Jan 17, 2019

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2938/

Build result: FAILURE

GitHub pull request #2117 of commit e356d64 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-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2117/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 52ad216 # timeout=10Checking out Revision 52ad216 (origin/pr/2117/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 52ad21614a0cd38b96984dd3d9d4db80af5c04b4First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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commented Jan 17, 2019

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2939/

Build result: FAILURE

GitHub pull request #2117 of commit ea845e8 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-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2117/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains f199257 # timeout=10Checking out Revision f199257 (origin/pr/2117/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f f199257b55db54f24faeb97ff5d5440e6a7d39f2First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@heuermh heuermh force-pushed the heuermh:genotype-annotation branch from ea845e8 to 05dbe0e Jan 17, 2019

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commented Jan 17, 2019

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2940/

Build result: FAILURE

GitHub pull request #2117 of commit 05dbe0e 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-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2117/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains e2bf834 # timeout=10Checking out Revision e2bf834 (origin/pr/2117/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f e2bf834e4bece92095fd1fa4ce35a9dbf496c887First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh added some commits Jan 14, 2019

wip

@heuermh heuermh force-pushed the heuermh:genotype-annotation branch from 05dbe0e to 049c95b Jan 20, 2019

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commented Jan 20, 2019

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2942/

Build result: FAILURE

GitHub pull request #2117 of commit 049c95b 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-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2117/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains b0e4b5c # timeout=10Checking out Revision b0e4b5c (origin/pr/2117/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f b0e4b5cf13d74c9d4e5f68ace980627a467fc465First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.11,2.2.3,ubuntuADAM-prb ? 2.7.5,2.11,2.2.3,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Filter supplemental reads from scoring
Currently a supplemental read can be added to the sum of base qualities
of a duplicate candidate, artificially inflating its base quality sum
when mark duplicates is trying to choose the best read from the bunch.

This is one (the simplest and most superficial) fix to the problem. Just
filter supplemental reads out when summing.

Another solution could be to use the supplemental flag when setting the
"not primary read flag" in SAMRecordConverter.

Yet another would be to create a separate field in SingleReadBucket for
supplemental reads.

Not sure what the downstream effects of these different approaches are.
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commented Mar 1, 2019

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2950/

Build result: FAILURE

GitHub pull request #2117 of commit 7cedede 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-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2117/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains b0c6028 # timeout=10Checking out Revision b0c6028 (origin/pr/2117/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f b0c6028b6c4c4b100fa172d7bb7f0b90d0fd84d9First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.11,2.2.3,ubuntuADAM-prb ? 2.7.5,2.11,2.2.3,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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