bigdatagenomics / adam / 2555

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jenkins

[ADAM-1402] Fix INDEL realigner bad binary search.

Resolves #1402. Includes fixes to consensus generator and reference scorer.

Improve INDEL realigner performance:

* Exit early when realigning will not yield a better score.
* Eliminate substring call in sweep over reference.
* Change datastructures to be immutable wherever possible.
* Add bound checking and other error checking.
* Rewrite target association code to use array instead of set, and improve load balancing.
* Delete high coverage targets with reduceByKey.

Additionally:
* Improve telemetry/logging to sort out load balance issue.
* Support using reference file in INDEL realignment.
* Log reads with negative alignment sizes.
* Improved test coverage for insertion realignment.
* Fix CIGARs on reads that partially overlap INDEL.
* Soft clip reads that partially align to an insertion.
* Eliminate non-determinism.
* Fixed reference file.
* Serialization fixes and debug.
* Fix bad score.
* Clean up clipping code?
* Unclip clipped reads.

299 of 299 new or added lines in 11 files covered. (100.0%)

4918 of 6028 relevant lines covered (81.59%)

6.52 hits per line