[ADAM-1753] Only emit realignment targets for reads containing a single INDEL

[fnothaft]

Resolves #1753. Not ready for merge, still validating.

[AmplabJenkins]

Test FAILed.
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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/1756/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 825c0e21e70c2672158c1a8d15370c25afc54aa6 # timeout=10Checking out Revision 825c0e21e70c2672158c1a8d15370c25afc54aa6 (origin/pr/1756/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 825c0e21e70c2672158c1a8d15370c25afc54aa6First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[fnothaft]

This is good to merge.

[heuermh]

Thank you, @fnothaft

[heuermh]

Sorry, Jenkins, I went a little too fast on this one ;)

[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/2421/
Test PASSed.