Refactor Genotype and GenotypeAnnotation #2117
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Test FAILed. Build result: FAILUREGitHub 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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Test FAILed. Build result: FAILUREGitHub 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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Test FAILed. Build result: FAILUREGitHub 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
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Test FAILed. Build result: FAILUREGitHub 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
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Test FAILed. Build result: FAILUREGitHub 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. |
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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Test FAILed. Build result: FAILUREGitHub 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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Closing as WontFix. Unfortunately there isn't a driver or reviewer for landing this large change. |
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Work in progress.
Companion pull request to bigdatagenomics/bdg-formats#176.