Parquet and indexed Parquet RDD implementations, and indices.

* Scala reimplementation of the Parquet footer parsing.

* Implementations of two Parquet-based RDDs

AvroParquetRDD.scala contains two RDD implementations around Parquet files.  The first,
AvroParquetRDD, reads a single Parquet file (containing an Avro schema) and partitions the RDD
based on the row groups of the file.

The second, AvroIndexedParquetRDD, is an implementation that reads an index across a set of
parquet files, determines (according to the predicate contained in CombinedFilter) which row groups
in which files are relevant to the query, and produces an RDD whose partitions are in 1-1 correspondence
with the matching row groups from the index.

The parquet_reimpl/index package contains the code necessary for reading and writing indices.

* Adding two CLI commands, including an index generation command.

Adding two new CLI commands:
1. IndexFlatGenotype, which reads in a flat genotype Parquet file, and produces the index for that file.
2. the PrintParquet, which reads a Parquet file and prints out a limited number of entries form the file.

(at the moment, the latter only supports ADAMFlatGenotype)

* Implemented ID/Range indices on Parquet files.
Merge pull request #267 from genomebridge/parquet-rebase

Parquet and indexed Parquet RDD implementations, and indices.
Use the scala.Console.out rather than System.out in PrintADAM

This seems to allow us to (in tests) redirect the output stream using the
Console.withOut command.
Added a failing test for Features2ADAM

Features2ADAM fails because it doesn't include an 'index' field in its
second command-line argument, and therefore Args4j can't parse the Features2ADAMArgs
object off a command line.
Added the missing 'index' argument to the Features2ADAMArgs class

Fixes the bug tested in the previous commit.