Variants Visualization #542
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Test FAILed. Build result: ABORTEDGitHub pull request #542 of commit c11fec6 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-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/adam.git # 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/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/542/merge^{commit} # timeout=10Checking out Revision 2578aa3 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 2578aa3 > git rev-list b409bd0004a00c2dac712b5c567963b3e013c8e3 # timeout=10Triggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 1.0.4,centosTriggering ADAM-prb ? 2.3.0,centosADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 1.0.4,centos completed with result ABORTEDADAM-prb ? 2.3.0,centos completed with result FAILURETest FAILed. |
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Jenkins, retest this please. |
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@fnothaft We really need to fix that intermittent wigFix bug :-/ |
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@laserson hah, yeah... I suppose we need to root-cause it first... |
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Test FAILed. Build result: ABORTEDGitHub pull request #542 of commit c11fec6 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-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/adam.git # 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/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/542/merge^{commit} # timeout=10Checking out Revision 2578aa3 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 2578aa3 > git rev-list b409bd0004a00c2dac712b5c567963b3e013c8e3 # timeout=10Triggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 1.0.4,centosTriggering ADAM-prb ? 2.3.0,centosADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 1.0.4,centos completed with result SUCCESSADAM-prb ? 2.3.0,centos completed with result ABORTEDTest FAILed. |
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@erictu Could you rebase this on master? |
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| if (args.inputPath.endsWith(".vcf")) { | ||
| VizReads.variants = sc.adamVCFLoad(args.inputPath).flatMap(_.genotypes) |
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A few small nits, but otherwise LGTM! |
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Test PASSed. |
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Test PASSed. |
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Merged! Thanks @erictu! |
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Working visualization of variants when given vcf input to ADAM viz
Also added loadGenotypes and maybeLoadVcf in ADAMContext