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-1834] Add proper extensions for SAM/BAM/CRAM output formats. #1835

Merged

Conversation

@fnothaft
Copy link
Member

@fnothaft fnothaft commented Dec 16, 2017

Resolves #1834.

@AmplabJenkins
Copy link

@AmplabJenkins AmplabJenkins commented Dec 16, 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/2517/

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/1835/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 4ffad35 # timeout=10Checking out Revision 4ffad35 (origin/pr/1835/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4ffad35f7bbc2693ad1c83b43423e550c8b1d55aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@fnothaft fnothaft force-pushed the fnothaft:issues/1834-sam-bam-extensions branch from 797fe02 to a96155d Dec 16, 2017
@AmplabJenkins
Copy link

@AmplabJenkins AmplabJenkins commented Dec 16, 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/2518/
Test PASSed.

@heuermh heuermh added this to the 0.23.0 milestone Dec 16, 2017
@heuermh
Copy link
Member

@heuermh heuermh commented Dec 16, 2017

Does this completely resolve #1834 or do we also need HadoopGenomics/Hadoop-BAM#176? I'm not sure exactly how the issue manifests itself.

@fnothaft
Copy link
Member Author

@fnothaft fnothaft commented Dec 16, 2017

@heuermh
Copy link
Member

@heuermh heuermh commented Dec 16, 2017

We need HadoopGenomics/Hadoop-BAM#176 for VCF.

I see, thanks.

@heuermh heuermh merged commit 66c53e3 into bigdatagenomics:master Dec 16, 2017
2 checks passed
2 checks passed
Codacy/PR Quality Review Good work! A positive pull request.
Details
default Merged build finished.
Details
@heuermh
Copy link
Member

@heuermh heuermh commented Dec 16, 2017

Thank you, @fnothaft!

@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

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