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Variants Visualization #542

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merged 1 commit into from Jan 22, 2015

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erictu commented Jan 9, 2015

Working visualization of variants when given vcf input to ADAM viz
Also added loadGenotypes and maybeLoadVcf in ADAMContext

@erictu erictu changed the title from Basic viz to Variants Visualization Jan 9, 2015

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Test FAILed.
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Build result: ABORTED

GitHub 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 FAILURE
Test FAILed.

AmplabJenkins commented Jan 9, 2015

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/523/

Build result: ABORTED

GitHub 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 FAILURE
Test FAILed.

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Jenkins, retest this please.

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laserson commented Jan 9, 2015

Jenkins, retest this please.

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@fnothaft We really need to fix that intermittent wigFix bug :-/

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laserson commented Jan 9, 2015

@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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fnothaft commented Jan 9, 2015

@laserson hah, yeah... I suppose we need to root-cause it first...

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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/524/

Build result: ABORTED

GitHub 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 ABORTED
Test FAILed.

AmplabJenkins commented Jan 10, 2015

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/524/

Build result: ABORTED

GitHub 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 ABORTED
Test FAILed.

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@erictu Could you rebase this on master?

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laserson commented Jan 10, 2015

@erictu Could you rebase this on master?

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fnothaft Jan 12, 2015

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Add a newline before EOF.

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fnothaft Jan 12, 2015

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Add a newline before EOF.

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A few small nits, but otherwise LGTM!

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fnothaft commented Jan 12, 2015

A few small nits, but otherwise LGTM!

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Test PASSed.
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Test PASSed.

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Test PASSed.
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Test PASSed.

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Test PASSed.
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Test PASSed.

AmplabJenkins commented Jan 22, 2015

Test PASSed.
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Test PASSed.

fnothaft added a commit that referenced this pull request Jan 22, 2015

@fnothaft fnothaft merged commit 8500f5a into bigdatagenomics:master Jan 22, 2015

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Merged! Thanks @erictu!

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fnothaft commented Jan 22, 2015

Merged! Thanks @erictu!

@fnothaft fnothaft referenced this pull request Jan 24, 2015

Closed

Simplify `ADAMContext` #553

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