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[ADAM-631] Allow VCF conversion to sort on output after coalescing. #632

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merged 1 commit into from Apr 2, 2015

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fnothaft commented Mar 26, 2015

Resolves #631. Renames adamVCFSave to saveAsVcf and adds hooks to optionally coalesce and sort during save. Sort is performed after coalescing. Sort and coalesce are independent.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #632 of commit e012d8c automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[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/632/merge^{commit} # timeout=10 > git branch -a --contains 955b802 # timeout=10 > git rev-parse remotes/origin/pr/632/merge^{commit} # timeout=10Checking out Revision 955b802 (origin/pr/632/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 955b8028588e263e5b8f73accd829de19e23de8aFirst time build. Skipping changelog.Triggering ADAM-prb ? 1.0.4,centosTriggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 2.3.0,centosADAM-prb ? 1.0.4,centos completed with result FAILUREADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 2.3.0,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub pull request #632 of commit e012d8c automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[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/632/merge^{commit} # timeout=10 > git branch -a --contains 955b802 # timeout=10 > git rev-parse remotes/origin/pr/632/merge^{commit} # timeout=10Checking out Revision 955b802 (origin/pr/632/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 955b8028588e263e5b8f73accd829de19e23de8aFirst time build. Skipping changelog.Triggering ADAM-prb ? 1.0.4,centosTriggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 2.3.0,centosADAM-prb ? 1.0.4,centos completed with result FAILUREADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 2.3.0,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Rebased.

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fnothaft commented Apr 2, 2015

Rebased.

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Test PASSed.
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Test PASSed.
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Test PASSed.

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Looks good, Frank. Thanks!

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massie commented Apr 2, 2015

Looks good, Frank. Thanks!

massie added a commit that referenced this pull request Apr 2, 2015

Merge pull request #632 from fnothaft/sort-vcf
[ADAM-631] Allow VCF conversion to sort on output after coalescing.

@massie massie merged commit 6281f8c into bigdatagenomics:master Apr 2, 2015

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