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Ignore VCF INFO fields with number=G when stringency=LENIENT #1935

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merged 1 commit into from Mar 5, 2018

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jpdna commented Mar 3, 2018

Ignores, and logs a warning, for non-specifically-supported INFO fields with Number=G when Stringency = LENIENT
rather than the current behavior of throwing IllegalArgumentException

Needed because I want to be able to parse directly the gnomAD VCF file contains tags such as:

INFO=<ID=GC_Male,Number=G,Type=Integer,Description="Count of Male individuals for each genotype">

These INFO number=G tags don't have a simple/general meaning for multi-allelic variants which are split when loaded to ADAM, which is why in status quo this produces IllegalArgumentException("Number=G INFO lines are not supported in split-allelic model: %s".
Simply allowing the user to choose to ignore INFO tags of number=G seems a workable solution to me.

Aside:
At the least, there is not a general solution for INFO Number=G fields that can be implemented in lineToVariantContextExtractor.
If we do decide that we want to do something specific for an INFO Number=G tag like GC_Male we can consider adding it as a supported tag and adding custom logic to parse it later.

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AmplabJenkins commented Mar 3, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2689/

Build result: FAILURE

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1935/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains f4d6e85 # timeout=10Checking out Revision f4d6e85 (origin/pr/1935/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f f4d6e854a8c8880fc2b71acdc827957021a9fd3dFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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coveralls commented Mar 3, 2018

Coverage Status

Coverage decreased (-0.04%) to 82.649% when pulling 0e09c6b on jpdna:split_vcf_info_g into babf839 on bigdatagenomics:master.

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AmplabJenkins commented Mar 3, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2690/

Build result: FAILURE

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1935/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 3bbbd7d # timeout=10Checking out Revision 3bbbd7d (origin/pr/1935/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 3bbbd7dc1bbe20b2f5271ec567a29bbd96ccbe19First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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jpdna commented Mar 3, 2018

Can one f you point me to where in the Jenkins output the relevant error is?
Tests pass for me locally.

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heuermh commented Mar 5, 2018

@jpdna This also passes tests for me locally, will try retriggering the Jenkins build.

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heuermh commented Mar 5, 2018

Jenkins, retest this please.

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AmplabJenkins commented Mar 5, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2693/
Test PASSed.

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heuermh approved these changes Mar 5, 2018

@heuermh heuermh requested a review from fnothaft Mar 5, 2018

@heuermh heuermh added this to the 0.24.0 milestone Mar 5, 2018

@fnothaft fnothaft merged commit 9cec595 into bigdatagenomics:master Mar 5, 2018

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Codacy/PR Quality Review Good work! A positive pull request.
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fnothaft commented Mar 5, 2018

Merged! Thanks @jpdna!

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