Adding a minor paren-related style change and a println
Merge pull request #102 from hammerlab/pretty-print-modification

Adding a minor paren-related style change and a println
The SomaticThresholdVariantCaller now filters non-variants out of the list of variants Closes #103
The SomaticThresholdVariantCaller now filters non-variants out of the list of variants Closes #103
Merge pull request #104 from hammerlab/somatic-threshold-duplicate-alleles

The SomaticThresholdVariantCaller now filters non-variants out of the list of variants Closes #103
Some refactoring and performance improvements.

Initial goal here was just to be able to run on chr20 without specifying -loci argument and still have things work (i.e. don't have two tasks stuck looking at other contigs that don't have reads). That ended up expanding a bit into a number of refactorings and code fixes.

 * Introduce ReadSet for keeping track of read metadata (e.g. sequence dictionaries) with the RDD[Read] instance.
 * paritionLociByApproximateReadDepth now has special handling of contigs with no reads mapped for better efficiency.
 * pileupFlatMap and variants now have a 'skipEmpty' option, which, if set, will result in skipping loci where no reads align. This can be an important optimization when running over e.g. many contigs that have no reads mapped. Add 'nextStartLocus' method to SlidingReadWindow to enable an efficient implementation of this.
 * SlidingReadWindow: more efficient setCurrentLocus implementation.
 * Minor convenience functions added to LociSet.
 * Add Read.InputFilters to have a single place to put filters for loading reads. Modified read loading functions to use it.
 * Add hasMdTag as a read filter.
 * Added -no-sequence-dictionary argument to specify that contigs and lengths should come directly from reads, not from the sequence dictionary.
 * Dropped some for loops (converted into foreach or while loops) for supposed performance improvement (not measured).
 * Specifying non-existent contigs / loci with the -loci argument results in an error. Closes #6.
 * Added runOnly hack to SparkTest to give us a way to run a single unit test.
 * README fix
DistributedUtil sorting / splitting of reads overhaul. Currently still fails on real data. Add test data and a failing test case for somatic thershold caller.
add debug output
Support for writing out genotypes to JSON format. Upgrade to Spark 1.0, Java 7, and ADAM 0.11.1-SNAPSHOT.
Fix dependency issue by moving hadoop to the end of the dependencies. Fix Kryo infinite recursion by calling setReferences(true) when registering serializers.
better comments