[ADAM-1551] Emit non-reference model genotype at called sites. #1559
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Test PASSed. |
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Test FAILed. 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. 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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Test PASSed. |
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Pinging for review. |
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We'll need to cut a bdg-formats release if this does look good to go. |
heuermh
approved these changes
Jun 21, 2017
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Thanks @heuermh for the review. I will cut bdg-formats 0.11.1 right now. |
Resolves bigdatagenomics#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.
…ly high Phred scores. Resolves bigdatagenomics#1569. Can support phred scores >1,000.
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This is ready to go from my side. |
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Test PASSed. |
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Thank you, @fnothaft |
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Resolves #1551. WIP. Still needs tests.