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[ADAM-1562] Index off by one for VCF genotype Number=A attributes. #1563

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merged 1 commit into from Jun 14, 2017

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heuermh commented Jun 9, 2017

Fixes #1562

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Coverage Status

Coverage increased (+0.2%) to 83.297% when pulling b65cb9a on heuermh:genotype-number-a into ad5ae6d on bigdatagenomics:master.

coveralls commented Jun 9, 2017

Coverage Status

Coverage increased (+0.2%) to 83.297% when pulling b65cb9a on heuermh:genotype-number-a into ad5ae6d on bigdatagenomics:master.

@fnothaft

LGTM! Thanks @heuermh!

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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/2092/

Build result: ABORTED

[...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/1563/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 0559070 # timeout=10Checking out Revision 0559070 (origin/pr/1563/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 0559070b9ec2a03179a36a183fe6a35c97bc31f8First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result ABORTEDADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result ABORTEDADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Jun 9, 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/2092/

Build result: ABORTED

[...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/1563/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 0559070 # timeout=10Checking out Revision 0559070 (origin/pr/1563/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 0559070b9ec2a03179a36a183fe6a35c97bc31f8First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result ABORTEDADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result ABORTEDADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@devin-petersohn

Looks great!

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fnothaft Jun 14, 2017

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Jenkins, retest this please.

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fnothaft commented Jun 14, 2017

Jenkins, retest this please.

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coveralls Jun 14, 2017

Coverage Status

Coverage increased (+0.2%) to 83.297% when pulling b65cb9a on heuermh:genotype-number-a into ad5ae6d on bigdatagenomics:master.

coveralls commented Jun 14, 2017

Coverage Status

Coverage increased (+0.2%) to 83.297% when pulling b65cb9a on heuermh:genotype-number-a into ad5ae6d on bigdatagenomics:master.

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2100/
Test PASSed.

AmplabJenkins commented Jun 14, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2100/
Test PASSed.

@fnothaft fnothaft merged commit c78a0ed into bigdatagenomics:master Jun 14, 2017

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codacy/pr Good work! A positive pull request.
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coverage/coveralls Coverage increased (+0.2%) to 83.297%
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default Merged build finished.
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Merged! Thanks @heuermh!

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fnothaft commented Jun 14, 2017

Merged! Thanks @heuermh!

@heuermh heuermh deleted the heuermh:genotype-number-a branch Jun 14, 2017

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017

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

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