Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[ADAM-1676] Add more finely grained validation for INFO/FORMAT fields. #1677

Merged

Conversation

@fnothaft
Copy link
Member

@fnothaft fnothaft commented Aug 22, 2017

Resolves #1676. Pushes validation checking down to the single field conversion level, which keeps a variant/genotype record around even if a bad INFO/FORMAT field was attached to that record.

WIP, needs more testing, not ready for merge.

@fnothaft fnothaft requested a review from heuermh Aug 22, 2017
@coveralls
Copy link

@coveralls coveralls commented Aug 22, 2017

Coverage Status

Coverage decreased (-0.5%) to 82.948% when pulling cf2aa38 on fnothaft:issues/1676-validate-fields into b46b583 on bigdatagenomics:master.

@AmplabJenkins
Copy link

@AmplabJenkins AmplabJenkins commented Aug 22, 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/2324/
Test PASSed.

@fnothaft
Copy link
Member Author

@fnothaft fnothaft commented Sep 6, 2017

Ping for review.

@heuermh
Copy link
Member

@heuermh heuermh commented Sep 6, 2017

The code here looks reasonable, I'm not sure the conversation in issue #1676 has been resolved.

@fnothaft fnothaft force-pushed the fnothaft:issues/1676-validate-fields branch from cf2aa38 to 31cd054 Sep 12, 2017
@fnothaft
Copy link
Member Author

@fnothaft fnothaft commented Sep 12, 2017

Rebased. Ready for merge once tests pass.

@AmplabJenkins
Copy link

@AmplabJenkins AmplabJenkins commented Sep 12, 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/2363/

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/1677/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 16f2efe # timeout=10Checking out Revision 16f2efe (origin/pr/1677/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 16f2efe3faa47ae85a79d0f8072f96e77b7db812First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,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 ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Resolves #1676. Pushes validation checking down to the single field conversion
level, which keeps a variant/genotype record around even if a bad INFO/FORMAT
field was attached to that record.
@fnothaft fnothaft force-pushed the fnothaft:issues/1676-validate-fields branch from 31cd054 to 84b5064 Sep 13, 2017
@AmplabJenkins
Copy link

@AmplabJenkins AmplabJenkins commented Sep 13, 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/2365/
Test PASSed.

@heuermh heuermh merged commit 547f92d into bigdatagenomics:master Sep 14, 2017
1 of 2 checks passed
1 of 2 checks passed
codacy/pr Not so good... This pull request quality could be better.
Details
default Merged build finished.
Details
@heuermh
Copy link
Member

@heuermh heuermh commented Sep 14, 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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
Linked issues

Successfully merging this pull request may close these issues.

None yet

4 participants
You can’t perform that action at this time.