Clean up INDEL allele check and filter nits for handling het alts

[fnothaft]

Resolves #245, #246, #247.

[coveralls]

Changes Unknown when pulling aa655661dd274d7d104772b93dc8a714df8881f0 on fnothaft:issues/245-246-247-start-indel-and-filters into on bigdatagenomics:master.

[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/195/ Test PASSed.

[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/196/

Build result: FAILURE

GitHub pull request #248 of commit f3def932d9a8e3f05e8070641101cab7fb169b42 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-staging-worker-02 (ubuntu 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/248/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains b97ae278b1acfe44911afd14655cfaf8a751b4fc # timeout=10Checking out Revision b97ae278b1acfe44911afd14655cfaf8a751b4fc (origin/pr/248/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f b97ae278b1acfe44911afd14655cfaf8a751b4fcFirst time build. Skipping changelog.Triggering avocado-prb » 2.6.0,2.11,2.0.0,centosTriggering avocado-prb » 2.3.0,2.11,2.0.0,centosTriggering avocado-prb » 2.3.0,2.10,2.0.0,centosTriggering avocado-prb » 2.6.0,2.10,2.0.0,centosavocado-prb » 2.6.0,2.11,2.0.0,centos completed with result FAILUREavocado-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 » 2.6.0,2.10,2.0.0,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/197/

Build result: FAILURE

GitHub pull request #248 of commit 3594741d8820c76bc7dca5cb794980c0c6281e55 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-staging-worker-02 (ubuntu 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/248/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains d90229f554197d67005a47317557614b6340fcdd # timeout=10Checking out Revision d90229f554197d67005a47317557614b6340fcdd (origin/pr/248/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f d90229f554197d67005a47317557614b6340fcddFirst time build. Skipping changelog.Triggering avocado-prb » 2.6.0,2.11,2.0.0,centosTriggering avocado-prb » 2.3.0,2.11,2.0.0,centosTriggering avocado-prb » 2.3.0,2.10,2.0.0,centosTriggering avocado-prb » 2.6.0,2.10,2.0.0,centosavocado-prb » 2.6.0,2.11,2.0.0,centos completed with result FAILUREavocado-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 » 2.6.0,2.10,2.0.0,centos completed with result FAILURE Test FAILed.

[coveralls]

Changes Unknown when pulling d7616354afa819035e94902b610148c9b43572d5 on fnothaft:issues/245-246-247-start-indel-and-filters into on bigdatagenomics:master.

[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/198/ Test PASSed.