[AVOCADO-274] Add flag to emit all genotyped variants, regardless of quality.

[fnothaft]

Resolves #274.

[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/220/

Build result: FAILURE

GitHub pull request #275 of commit 1ce218bfc0e5213d47965721ae40e7614462ef9b 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/275/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 756ef9131fcb00a0ff8346e331f3cf4e35b1966c # timeout=10Checking out Revision 756ef9131fcb00a0ff8346e331f3cf4e35b1966c (origin/pr/275/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 756ef9131fcb00a0ff8346e331f3cf4e35b1966cFirst 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 FAILUREavocado-prb » 2.6.0,2.11,2.0.0,centos completed with result FAILUREavocado-prb » 2.3.0,2.10,2.0.0,centos completed with result FAILUREavocado-prb » 2.3.0,2.11,2.0.0,centos completed with result FAILURE Test FAILed.