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[ADAM-1834] Add proper extensions for SAM/BAM/CRAM output formats. #1835

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merged 1 commit into from Dec 16, 2017

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fnothaft commented Dec 16, 2017

Resolves #1834.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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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/1835/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 4ffad35 # timeout=10Checking out Revision 4ffad35 (origin/pr/1835/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4ffad35f7bbc2693ad1c83b43423e550c8b1d55aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Dec 16, 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/2517/

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/1835/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 4ffad35 # timeout=10Checking out Revision 4ffad35 (origin/pr/1835/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4ffad35f7bbc2693ad1c83b43423e550c8b1d55aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Test PASSed.
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Test PASSed.

AmplabJenkins commented Dec 16, 2017

Test PASSed.
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Test PASSed.

@heuermh heuermh added this to the 0.23.0 milestone Dec 16, 2017

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Does this completely resolve #1834 or do we also need HadoopGenomics/Hadoop-BAM#176? I'm not sure exactly how the issue manifests itself.

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heuermh commented Dec 16, 2017

Does this completely resolve #1834 or do we also need HadoopGenomics/Hadoop-BAM#176? I'm not sure exactly how the issue manifests itself.

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fnothaft commented Dec 16, 2017

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We need HadoopGenomics/Hadoop-BAM#176 for VCF.

I see, thanks.

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heuermh commented Dec 16, 2017

We need HadoopGenomics/Hadoop-BAM#176 for VCF.

I see, thanks.

@heuermh heuermh merged commit 66c53e3 into bigdatagenomics:master Dec 16, 2017

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Codacy/PR Quality Review Good work! A positive pull request.
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Thank you, @fnothaft!

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heuermh commented Dec 16, 2017

Thank you, @fnothaft!

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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