Commits on Mar 31, 2017

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

   Resolves bigdatagenomics#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.

   

   fnothaft committed Mar 31, 2017
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