Pass assembly variants to realigner as knowns

[fnothaft]

Resolves #200.

[AmplabJenkins]

Test FAILed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/165/

Build result: FAILURE

GitHub pull request #208 of commit a3d1d49e602265ba80b27894ed38a88c64a4788d automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-02 (centos spark-test spark-compile) in workspace /home/jenkins/workspace/avocado-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/avocado.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/208/merge^{commit} # timeout=10 > git branch -a --contains 138d857103632c20f2cf04f87ea7fb072a771aa2 # timeout=10 > git rev-parse remotes/origin/pr/208/merge^{commit} # timeout=10Checking out Revision 138d857103632c20f2cf04f87ea7fb072a771aa2 (origin/pr/208/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 138d857103632c20f2cf04f87ea7fb072a771aa2First time build. Skipping changelog.Triggering avocado-prb ? 2.6.0,2.10,1.5.2,centosTriggering avocado-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting... Test FAILed.

[coveralls]

Coverage increased (+1.3%) to 85.166% when pulling 45c974d009ef80faa3487d4870d61207fde82b22 on fnothaft:issues/200-assembly-variants-to-realigner into de2522d5e0f6f7a48e6ff718f4df14bd80a1df41 on bigdatagenomics:master.

[AmplabJenkins]

Test FAILed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/174/

Build result: FAILURE

[...truncated 8 lines...] > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/208/merge^{commit} # timeout=10 > git branch -a --contains bf417147789e1afce1f0e703de95e0a4c770d455 # timeout=10 > git rev-parse remotes/origin/pr/208/merge^{commit} # timeout=10Checking out Revision bf417147789e1afce1f0e703de95e0a4c770d455 (origin/pr/208/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f bf417147789e1afce1f0e703de95e0a4c770d455First time build. Skipping changelog.Triggering avocado-prb ? 2.6.0,2.11,2.0.0,centosTriggering avocado-prb ? 2.3.0,2.10,2.0.0,centosTriggering avocado-prb ? 2.6.0,2.10,2.0.0,centosTriggering avocado-prb ? 2.6.0,2.11,1.6.1,centosTriggering avocado-prb ? 2.3.0,2.10,1.6.1,centosTriggering avocado-prb ? 2.3.0,2.11,2.0.0,centosTriggering avocado-prb ? 2.3.0,2.11,1.6.1,centosTriggering avocado-prb ? 2.6.0,2.10,1.6.1,centosavocado-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSavocado-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREavocado-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSavocado-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSavocado-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSavocado-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSavocado-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSavocado-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESS Test FAILed.