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[CANNOLI-43] Use accumulator for VCF header lines. #72

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merged 1 commit into from Feb 8, 2018

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heuermh commented Sep 15, 2017

Fixes #43
Depends on bigdatagenomics/adam#1727

Work in progress, currently Spark 2.x only due to AccumulatorAccumulatorV2 deprecation. I suggest waiting until ADAM post-0.23.0 when Spark 1.x support is dropped rather than trying to conditionally support both APIs.

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AmplabJenkins commented Sep 15, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/cannoli-prb/68/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/cannoli.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/72/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains c67f8b2 # timeout=10Checking out Revision c67f8b2 (origin/pr/72/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f c67f8b2ee8f45a4279ee4a898d22e093d6c4eeebFirst time build. Skipping changelog.Triggering cannoli-prb ? 2.3.0,2.11,1.6.1,centosTriggering cannoli-prb ? 2.6.0,2.10,2.0.0,centosTriggering cannoli-prb ? 2.6.0,2.11,2.0.0,centosTriggering cannoli-prb ? 2.6.0,2.10,1.6.1,centosTriggering cannoli-prb ? 2.3.0,2.10,1.6.1,centosTriggering cannoli-prb ? 2.3.0,2.10,2.0.0,centosTriggering cannoli-prb ? 2.6.0,2.11,1.6.1,centosTriggering cannoli-prb ? 2.3.0,2.11,2.0.0,centoscannoli-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREcannoli-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREcannoli-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREcannoli-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREcannoli-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREcannoli-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREcannoli-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREcannoli-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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heuermh commented Jan 24, 2018

@fnothaft Should we merge this and bump the ADAM dependency to 0.24.0-SNAPSHOT, which would allow us to drop Spark 1.x and Scala 2.10 support here, or did you want to release Cannoli against ADAM 0.23.0 first?

@heuermh heuermh force-pushed the heuermh:issue-43 branch from d5b4e05 to cc390a0 Jan 24, 2018

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AmplabJenkins commented Jan 24, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/cannoli-prb/91/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/cannoli.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/72/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 36fe46d # timeout=10Checking out Revision 36fe46d (origin/pr/72/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 36fe46d2399e691ce17db2e58f2f993dd9bee9f7First time build. Skipping changelog.Triggering cannoli-prb ? 2.3.0,2.10,1.6.1,centosTriggering cannoli-prb ? 2.6.0,2.11,2.0.0,centosTriggering cannoli-prb ? 2.6.0,2.10,2.0.0,centosTriggering cannoli-prb ? 2.6.0,2.10,1.6.1,centosTriggering cannoli-prb ? 2.3.0,2.10,2.0.0,centosTriggering cannoli-prb ? 2.3.0,2.11,1.6.1,centosTriggering cannoli-prb ? 2.3.0,2.11,2.0.0,centosTriggering cannoli-prb ? 2.6.0,2.11,1.6.1,centoscannoli-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREcannoli-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREcannoli-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREcannoli-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREcannoli-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREcannoli-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREcannoli-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREcannoli-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@heuermh heuermh added this to the 0.2.0 milestone Jan 24, 2018

@heuermh heuermh force-pushed the heuermh:issue-43 branch from cc390a0 to ec5bf11 Feb 8, 2018

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AmplabJenkins commented Feb 8, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/cannoli-prb/100/
Test PASSed.

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coveralls commented Feb 8, 2018

Coverage Status

Coverage increased (+0.01%) to 31.605% when pulling ec5bf11 on heuermh:issue-43 into 7c16def on bigdatagenomics:master.

@heuermh heuermh merged commit 276be85 into bigdatagenomics:master Feb 8, 2018

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@heuermh heuermh deleted the heuermh:issue-43 branch Feb 8, 2018

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