sort reads locally on each task
remove count() operation in writeVariants
add take() method to LociSet and LociMap
Implement loci partitioning by approximate read depth.
formatting
fixes for depth-based loci partitioning, very basic unit tests, refactoring
unit test fix
turn on spark speculation in scripts/guacamole-demeter
bayesian quality based caller
Change partitionLociByApproximateReadDepth to take an 'accuracy' factor instead of numMicroPartitions, and include a progress message on read depth across micro partitions.  Better comments.
change partitioningAccuracy default to 250
fix up mdtags in tests and test actual variant
calculate distribution of reads across tasks (to understand skew) and output it at the end of each run
Merge pull request #65 from hammerlab/dist-debug-may-15

partition loci by read depth
Merge pull request #67 from hammerlab/build-ref-bug

Fix up mdtags in tests and test actual variant
fix merge conflict
Merge pull request #66 from hammerlab/quality-caller

Variant caller based on the quality scores
fix merge conflict
add uniformbayes as possible caller
add caller name to spark context app name