Initial implementation of base quality score recalibration. The tables are currently tested, but until we have RDD and Broadcast mockups it's hard to test the rest. Beware any results coming from this tool until such time as its components are fully tested.
Allow 'N' bases to be complemented. Gzip the dbsnp resource so it fits within Github file limits.
Enable downsampling in transforms
Scalability and bugfixes for BQSRv1
 - dbSNP no longer passed into ReadCovariates numbers -- this was making each record about 1G of data. Now each position is looked up in dbSNP at object creation.
 - Better encapsulation of functions.
 - QualByRG needs the read groups up front -- some nodes may (stochastically) only see a strict subset of readgroups.