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[ADAM-1551] Emit non-reference model genotype at called sites. #1559

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merged 4 commits into from Jun 22, 2017

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fnothaft commented Jun 7, 2017

Resolves #1551. WIP. Still needs tests.

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Coverage Status

Coverage increased (+0.3%) to 83.405% when pulling d26a6d5 on fnothaft:issues/1551-gvcf-nonref-at-variant-sites into ad5ae6d on bigdatagenomics:master.

coveralls commented Jun 7, 2017

Coverage Status

Coverage increased (+0.3%) to 83.405% when pulling d26a6d5 on fnothaft:issues/1551-gvcf-nonref-at-variant-sites into ad5ae6d on bigdatagenomics:master.

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Test PASSed.
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Test FAILed.
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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/1559/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains f0338eb9c189ed9a14a10585448b708571a9a2dc # timeout=10Checking out Revision f0338eb9c189ed9a14a10585448b708571a9a2dc (origin/pr/1559/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f f0338eb9c189ed9a14a10585448b708571a9a2dcFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Jun 19, 2017

Test FAILed.
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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/1559/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains f0338eb9c189ed9a14a10585448b708571a9a2dc # timeout=10Checking out Revision f0338eb9c189ed9a14a10585448b708571a9a2dc (origin/pr/1559/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f f0338eb9c189ed9a14a10585448b708571a9a2dcFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Test FAILed.
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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/1559/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 846edd5b75f067df8d50b4247f7a76b3ce077435 # timeout=10Checking out Revision 846edd5b75f067df8d50b4247f7a76b3ce077435 (origin/pr/1559/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 846edd5b75f067df8d50b4247f7a76b3ce077435First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Jun 19, 2017

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/1559/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 846edd5b75f067df8d50b4247f7a76b3ce077435 # timeout=10Checking out Revision 846edd5b75f067df8d50b4247f7a76b3ce077435 (origin/pr/1559/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 846edd5b75f067df8d50b4247f7a76b3ce077435First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Coverage Status

Coverage decreased (-0.3%) to 83.034% when pulling 32b9620 on fnothaft:issues/1551-gvcf-nonref-at-variant-sites into 152a8ad on bigdatagenomics:master.

coveralls commented Jun 19, 2017

Coverage Status

Coverage decreased (-0.3%) to 83.034% when pulling 32b9620 on fnothaft:issues/1551-gvcf-nonref-at-variant-sites into 152a8ad on bigdatagenomics:master.

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Test PASSed.
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fnothaft Jun 21, 2017

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Pinging for review.

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fnothaft commented Jun 21, 2017

Pinging for review.

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fnothaft Jun 21, 2017

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We'll need to cut a bdg-formats release if this does look good to go.

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fnothaft commented Jun 21, 2017

We'll need to cut a bdg-formats release if this does look good to go.

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fnothaft Jun 21, 2017

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Thanks @heuermh for the review. I will cut bdg-formats 0.11.1 right now.

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fnothaft commented Jun 21, 2017

Thanks @heuermh for the review. I will cut bdg-formats 0.11.1 right now.

fnothaft added some commits Jun 7, 2017

[ADAM-1568] Fix gVCF reference model import/export code.
Resolves #1568. Fixes a bug where the wrong non-reference allele index was set
for multiallelic sites with >1 known alternate allele and a non-reference model.
[ADAM-1569] Support log space probabilities in PhredUtils for extreme…
…ly high Phred scores.

Resolves #1569. Can support phred scores >1,000.
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This is ready to go from my side.

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fnothaft commented Jun 22, 2017

This is ready to go from my side.

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coveralls Jun 22, 2017

Coverage Status

Coverage decreased (-0.3%) to 83.046% when pulling 8cf09f6 on fnothaft:issues/1551-gvcf-nonref-at-variant-sites into 310d9f9 on bigdatagenomics:master.

coveralls commented Jun 22, 2017

Coverage Status

Coverage decreased (-0.3%) to 83.046% when pulling 8cf09f6 on fnothaft:issues/1551-gvcf-nonref-at-variant-sites into 310d9f9 on bigdatagenomics:master.

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Coverage Status

Coverage decreased (-0.8%) to 82.601% when pulling 8cf09f6 on fnothaft:issues/1551-gvcf-nonref-at-variant-sites into 310d9f9 on bigdatagenomics:master.

coveralls commented Jun 22, 2017

Coverage Status

Coverage decreased (-0.8%) to 82.601% when pulling 8cf09f6 on fnothaft:issues/1551-gvcf-nonref-at-variant-sites into 310d9f9 on bigdatagenomics:master.

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Test PASSed.
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Test PASSed.

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@heuermh heuermh merged commit a4b4ef0 into bigdatagenomics:master Jun 22, 2017

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codacy/pr Not so good... This pull request quality could be better.
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coverage/coveralls Coverage decreased (-0.3%) to 83.046%
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heuermh Jun 22, 2017

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Thank you, @fnothaft

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heuermh commented Jun 22, 2017

Thank you, @fnothaft

@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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