Merge pull request #78 from jey/spark-0.9-upgrade

Upgrade to Spark 0.9 and Scala 2.10
Refactoring FASTA work to break contig sizes.
Merge pull request #160 from fnothaft/fix-fasta-large

Refactoring FASTA work to break contig sizes.
fix typo in log4j config, but junk is still spewed to stdout
Remove existing BQSR implementation
Make quality scores into ints
Scaffolding for BQSR implementation
add Util.hashCombine
add stuff to Observation
Make ObservationTable ctor private
ObservationTable fixes/changes
Empirical error probability tweaks
Don't need to broadcast SnpTable; it's only referenced once
add Recalibrator skeleton
Rename PhredQualityScore to QualityScore
ObservationTable fixes
ObservationTable doesn't need to be sorted
adjust variable naming
split out readGroup and quality covariates
Clean up covariates a bit