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Add optional accumulator for VCF header lines to VCFOutFormatter. #1727

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merged 1 commit into from Jan 24, 2018

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heuermh commented Sep 15, 2017

Required for bigdatagenomics/cannoli#43.

Work in progress, currently Spark 2.x only due to AccumulatorAccumulatorV2 deprecation. I suggest waiting until 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/ADAM-prb/2380/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1727/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 1303bd4 # timeout=10Checking out Revision 1303bd4 (origin/pr/1727/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 1303bd449f596f3aa037ebd4dfd90d377c114184First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@heuermh heuermh added this to the 0.24.0 milestone Nov 29, 2017

@heuermh heuermh added this to Triage in Release 0.24.0 Jan 4, 2018

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heuermh commented Jan 9, 2018

Rebased.

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coveralls commented Jan 9, 2018

Coverage Status

Coverage decreased (-0.006%) to 82.815% when pulling 3a8c627 on heuermh:out-formatter-accumulator into 71f9d13 on bigdatagenomics:master.

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AmplabJenkins commented Jan 9, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2555/
Test PASSed.

@fnothaft

LGTM! Before I merge, have you run this recently on the cluster?

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fnothaft commented Jan 22, 2018

Ping @heuermh

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heuermh commented Jan 22, 2018

have you run this recently on the cluster?

I have not, I'll set up to do that this afternoon.

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heuermh commented Jan 23, 2018

have you run this recently on the cluster?

Yes, I've confirmed this works on the cluster.

@fnothaft fnothaft merged commit c5b4ebc into bigdatagenomics:master Jan 24, 2018

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Codacy/PR Quality Review Good work! A positive pull request.
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fnothaft commented Jan 24, 2018

Merged! Thanks @heuermh!

@heuermh heuermh deleted the heuermh:out-formatter-accumulator branch Jan 24, 2018

@heuermh heuermh moved this from Triage to Completed in Release 0.24.0 Feb 10, 2018

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