[AVOCADO-272] Support variable copy number when genotyping.

[fnothaft]

Resolves #272.

[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/218/

Build result: FAILURE

GitHub pull request #273 of commit 4583d4f926e4ad8e957a55849b55605522d3799f automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-staging-worker-02 (ubuntu staging-02 staging) 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/273/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 3b9adf10c4a5652c1b5c83e337a3c3ef48f04428 # timeout=10Checking out Revision 3b9adf10c4a5652c1b5c83e337a3c3ef48f04428 (origin/pr/273/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3b9adf10c4a5652c1b5c83e337a3c3ef48f04428First time build. Skipping changelog.Triggering avocado-prb » 2.3.0,2.11,2.0.0,centosTriggering avocado-prb » 2.3.0,2.10,2.0.0,centosTriggering avocado-prb » 2.6.0,2.11,2.0.0,centosTriggering avocado-prb » 2.6.0,2.10,2.0.0,centosavocado-prb » 2.3.0,2.11,2.0.0,centos completed with result FAILUREavocado-prb » 2.3.0,2.10,2.0.0,centos completed with result FAILUREavocado-prb » 2.6.0,2.11,2.0.0,centos completed with result FAILUREavocado-prb » 2.6.0,2.10,2.0.0,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/avocado-prb/219/

Build result: FAILURE

GitHub pull request #273 of commit 4583d4f926e4ad8e957a55849b55605522d3799f automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-staging-worker-02 (ubuntu staging-02 staging) 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/273/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 3b9adf10c4a5652c1b5c83e337a3c3ef48f04428 # timeout=10Checking out Revision 3b9adf10c4a5652c1b5c83e337a3c3ef48f04428 (origin/pr/273/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3b9adf10c4a5652c1b5c83e337a3c3ef48f04428First time build. Skipping changelog.Triggering avocado-prb » 2.3.0,2.11,2.0.0,centosTriggering avocado-prb » 2.3.0,2.10,2.0.0,centosTriggering avocado-prb » 2.6.0,2.11,2.0.0,centosTriggering avocado-prb » 2.6.0,2.10,2.0.0,centosavocado-prb » 2.3.0,2.11,2.0.0,centos completed with result FAILUREavocado-prb » 2.3.0,2.10,2.0.0,centos completed with result FAILUREavocado-prb » 2.6.0,2.11,2.0.0,centos completed with result FAILUREavocado-prb » 2.6.0,2.10,2.0.0,centos completed with result FAILURE Test FAILed.

[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/221/

Build result: FAILURE

GitHub pull request #273 of commit f6196f87df9a9cc20880e5fdfe565162a94031f1 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-staging-worker-02 (ubuntu staging-02 staging) 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/273/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 93bbb211fc929e2b75049578dfafe49bfbf9d16c # timeout=10Checking out Revision 93bbb211fc929e2b75049578dfafe49bfbf9d16c (origin/pr/273/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 93bbb211fc929e2b75049578dfafe49bfbf9d16cFirst time build. Skipping changelog.Triggering avocado-prb » 2.6.0,2.10,2.0.0,centosTriggering avocado-prb » 2.6.0,2.11,2.0.0,centosTriggering avocado-prb » 2.3.0,2.10,2.0.0,centosTriggering avocado-prb » 2.3.0,2.11,2.0.0,centosavocado-prb » 2.6.0,2.10,2.0.0,centos completed with result SUCCESSavocado-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 » 2.3.0,2.11,2.0.0,centos completed with result SUCCESS Test FAILed.

[AmplabJenkins]

Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/222/ Test PASSed.

[AmplabJenkins]

Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/223/ Test PASSed.

[AmplabJenkins]

Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/227/ Test PASSed.