Fixing the README example to output a VCF
Merge pull request #100 from hammerlab/readme-vcf

Fixing the README example to output a VCF
Pretty print to stdout when the -out argument is not passed in
Merge pull request #101 from hammerlab/json-pretty

Pretty print to stdout when the -out argument is not passed in
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.