Pass assembly variants to realigner as knowns #208
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Test FAILed. Build result: FAILUREGitHub pull request #208 of commit a3d1d49 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-02 (centos spark-test spark-compile) in workspace /home/jenkins/workspace/avocado-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/avocado.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/208/merge^{commit} # timeout=10 > git branch -a --contains 138d857 # timeout=10 > git rev-parse remotes/origin/pr/208/merge^{commit} # timeout=10Checking out Revision 138d857 (origin/pr/208/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 138d857103632c20f2cf04f87ea7fb072a771aa2First time build. Skipping changelog.Triggering avocado-prb ? 2.6.0,2.10,1.5.2,centosTriggering avocado-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Test FAILed. |
Resolves bigdatagenomics#200. Depends on bigdatagenomics/adam#1363. * Adds a ConsensusRealigner that uses the main Realigner to realign reads, which are then fed into the variant discovery engine with loose filters. Any INDEL variants that are discovered are then fed in to ADAM's INDEL realignment engine as known INDELs. * Uses this realignment mode in the BiallelicGenotyperSuite to clean up a previously failing test. * Adds this to the Reassemble CLI as a `-use_consensus_realigner` switch.
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Test FAILed. Build result: FAILURE[...truncated 8 lines...] > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/208/merge^{commit} # timeout=10 > git branch -a --contains bf41714 # timeout=10 > git rev-parse remotes/origin/pr/208/merge^{commit} # timeout=10Checking out Revision bf41714 (origin/pr/208/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f bf417147789e1afce1f0e703de95e0a4c770d455First time build. Skipping changelog.Triggering avocado-prb ? 2.6.0,2.11,2.0.0,centosTriggering avocado-prb ? 2.3.0,2.10,2.0.0,centosTriggering avocado-prb ? 2.6.0,2.10,2.0.0,centosTriggering avocado-prb ? 2.6.0,2.11,1.6.1,centosTriggering avocado-prb ? 2.3.0,2.10,1.6.1,centosTriggering avocado-prb ? 2.3.0,2.11,2.0.0,centosTriggering avocado-prb ? 2.3.0,2.11,1.6.1,centosTriggering avocado-prb ? 2.6.0,2.10,1.6.1,centosavocado-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSavocado-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREavocado-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSavocado-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSavocado-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSavocado-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSavocado-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSavocado-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSTest FAILed. |
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Resolves #200.