[ADAM-1834] Add proper extensions for SAM/BAM/CRAM output formats.

[fnothaft]

Resolves #1834.

[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/2517/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1835/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 4ffad35 # timeout=10Checking out Revision 4ffad35 (origin/pr/1835/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4ffad35f7bbc2693ad1c83b43423e550c8b1d55aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
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/ADAM-prb/2518/
Test PASSed.

[heuermh]

Does this completely resolve #1834 or do we also need HadoopGenomics/Hadoop-BAM#176? I'm not sure exactly how the issue manifests itself.

[fnothaft]

We need HadoopGenomics/Hadoop-BAM#176 for VCF.

[heuermh]

We need HadoopGenomics/Hadoop-BAM#176 for VCF.

I see, thanks.

[heuermh]

Thank you, @fnothaft!