bigdatagenomics / adam / 2525

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[ADAM-1358] Refactor BQSR to improve performance and legibility.

Resolves #1358.

* Adds instrumentation to BQSR.
* Changed SnpTable to remove RichVariant conversion, use VariantRDD API.
* Refactoring SnpTable to eliminate per-residue costly masked site lookup.
* Restructuring core of SnpTable around an array to improve GC performance.
  Additionally, wrote custom serializer to improve serialization performance.
* Added test suite for SnpTable, to test table creation.
* Refactored SnpTable to use an IntervalArray-like approach. This approach
  improves masked site lookup performance by 50%.
* Added tests to SnpTableSuite to cover lookup case, and reenabled tests in
  BaseQualityRecalibrationSuite.
* Adding unit test coverage to covariates
* Revert "[ADAM-775] Allow all IUPAC codes in BQSR"
  This reverts commit 207eebaf3.
* Pulled Seq allocation for base check out into an immutable set.
* Rewrote dinuc covariate. 50% improvement in performance.
* Rewrite main BQSR aggregate as reduce by key
* Added tests to recalibrator, recalibration table.
* Majorly refactors of BQSR tables.
* Starting to factor out the QualityScore class
* Refactoring CovariateKey to reduce size in memory
* Eliminated `org.bdgenomics.adam.rich.DecadentRead` (partially resolves #577)
* Refactor CovariateKey to store record group ID instead of record group name.
* Removed `org.bdgenomics.adam.models.QualityScore`.
* Split multi-class files into one class per file (excepting private classes) to improve navigability.
* Scaladoc all the recalibrators! You get a scaladoc! And you get a scaladoc!

311 of 311 new or added lines in 16 files covered. (100.0%)

4695 of 5826 relevant lines covered (80.59%)

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