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

[fnothaft]

Resolves #2059.

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2827/

Build result: FAILURE

[...truncated 3 lines...]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/2061/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 9c5ec04 # timeout=10Checking out Revision 9c5ec04 (origin/pr/2061/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 9c5ec04c071042044aaf091dee198d8dbf16f4f6First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,2.2.2,ubuntuTriggering ADAM-prb ? 2.7.3,2.11,2.2.2,ubuntuADAM-prb ? 2.6.2,2.11,2.2.2,ubuntu completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[heuermh]

Closing in favor of #2075