Create test suite for FlagStat

[beaunorgeot]

Issue #355

[AmplabJenkins]

Can one of the admins verify this patch?

[fnothaft]

Jenkins, add to whitelist and test this please.

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/548/

Build result: FAILURE

GitHub pull request #552 of commit a7b5775 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/552/merge^{commit} # timeout=10Checking out Revision d7bae96 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f d7bae96 > git rev-list d8e02d9 # timeout=10Triggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 1.0.4,centosTriggering ADAM-prb ? 2.3.0,centosADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 1.0.4,centos completed with result FAILUREADAM-prb ? 2.3.0,centos completed with result FAILURE
Test FAILed.

[massie]

This is throwing an NPE which most likely means that getResource is returning null. Does the features/NA12878.adam file exist?

[fnothaft]

Looks like they meant to add it to the commit but forgot it. Good catch @massie!

Also @beaunorgeot, when you add it, can you add NA12878.adam as a SAM file? We try to keep the test resources as text files instead of binary files where possible (I believe there are a few small exceptions, but we try to limit those), as git handles text files better, and it also makes debugging tests a bit easier (you have the text and don't need to poke into a binary file).

[fnothaft]

A few small nits, but otherwise looks good to me! Thanks for putting this together, and I look forward to getting it merged in.

[massie]

Thanks @beaunorgeot. We always like to see more test coverage. 👍

[beaunorgeot]

Hi Guys, all requested changes/additions have been added. We're excited to be a part of ADAM! Keep us posted if there are further issues

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/553/

Build result: ABORTED

GitHub pull request #552 of commit 6dd4357 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/552/merge^{commit} # timeout=10Checking out Revision 598bd9f (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 598bd9f > git rev-list d8e02d9 # timeout=10Triggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.3.0,centos completed with result ABORTEDADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 1.0.4,centos completed with result FAILURE
Test FAILed.

[fnothaft]

Jenkins, retest this please.

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/554/

Build result: FAILURE

GitHub pull request #552 of commit 6dd4357 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/552/merge^{commit} # timeout=10Checking out Revision 598bd9f (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 598bd9f > git rev-list d8e02d9 # timeout=10Triggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.3.0,centos completed with result FAILUREADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 1.0.4,centos completed with result FAILURE
Test FAILed.

[fnothaft]

This just needs this:

./scripts/format-source

I will do that manually and commit.

[fnothaft]

Merged manually by f109a97.

[fnothaft]

Thanks @beaunorgeot!

[beaunorgeot]

Happy to be contributing. Lots of credit to @ansalaza on this one