Remove back reference between VariantAnnotation and Variant

[heuermh]

Fallout from removing back reference between VariantAnnotation and Variant as in bigdatagenomics/bdg-formats#117.

The forward reference between Variant and VariantAnnotation will be developed in #1288.

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /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 -c core.askpass=true 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 -c core.askpass=true 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/1297/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains dee3d2688a23636efc150f4d6fc05934e9f0fea9 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1297/merge^{commit} # timeout=10Checking out Revision dee3d2688a23636efc150f4d6fc05934e9f0fea9 (origin/pr/1297/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f dee3d2688a23636efc150f4d6fc05934e9f0fea9First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[heuermh]

@fnothaft any clue what this test failure is about? I've never looked at the flatten-related stuff before.

[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/1651/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /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 -c core.askpass=true 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 -c core.askpass=true 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/1297/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 378c6f0563b04909425430ce0698fe0a80365de8 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1297/merge^{commit} # timeout=10Checking out Revision 378c6f0563b04909425430ce0698fe0a80365de8 (origin/pr/1297/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 378c6f0563b04909425430ce0698fe0a80365de8First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[fnothaft]

LGTM! Let me give the Flatten failure a gander...

[AmplabJenkins]

Test PASSed.
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Test PASSed.

[fnothaft]

@heuermh what do we want the merge sequence to be with this PR? If you've got some time this morning, perhaps we could chat real quick?

[heuermh]

If you've got some time this morning, perhaps we could chat real quick?

Yep, let me know when and where

[fnothaft]

If you've got some time this morning, perhaps we could chat real quick?

Yep, let me know when and where

Just shot you a bluejeans link to your Gmail. Call on in whenever you're free.

[fnothaft]

Cherry-picked over to #1288 as 2398aa2.

[heuermh]

Thank you!