[ADAM-2059] Properly pass back primitive typed arrays to HTSJDK.

[heuermh]

Fixes #2059

Alt pull request to #2061, cherry-picked on top of #2072 and fixed unit test.

[AmplabJenkins]

Test FAILed.
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Build result: FAILURE

GitHub pull request #2075 of commit 6682107 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.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 > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2075/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 9c5fcc7 # timeout=10Checking out Revision 9c5fcc7 (origin/pr/2075/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 9c5fcc7dbb7cda20f8716be5c20e9410453bb92aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[coveralls]

Coverage increased (+0.06%) to 79.206% when pulling bd9da4a on heuermh:alt-issue-2059 into f3ec463 on bigdatagenomics:master.

[AmplabJenkins]

Test PASSed.
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Test PASSed.

[heuermh]

@akmorrow13 Ping for merge after Jenkins build completes

[AmplabJenkins]

Test PASSed.
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Test PASSed.

[akmorrow13]

Thanks @heuermh!