Added global Parquet logging in ADAMMain, with user specification
Merge pull request #271 from karenfeng/logging-command

Consolidate Parquet logging configuration
Adding k-mer and q-mer counting.
Merge pull request #269 from fnothaft/count-kmers-qmers

Adding k-mer and q-mer counting.
Created command categories
Fixes issue in reference models where strings are not sanitized on collection from avro.
Merge pull request #272 from karenfeng/command-categories

Created command categories
Merge pull request #273 from fnothaft/sanitize-reference-name

Fixes issue in reference models where strings are not sanitized on collection from avro.
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.

Added an IDRangeIndexGenerator implementation.
Updating IndexFlatGenotype to generate the IDRangeIndex entries.
Updating S3AvroParquetRDD to use the IDRangeIndex
Fixed the tests for S3AvroIndexedParquetRDD
Removed two old test suites.
Adding ParquetLister tests.
Added explanatory comments to CombinedFilter
Deleted HashIndex, which was old and wasn't being used.
Adding comments to AvroIndexedParquetRDD
Making IndexFlatGenotype Spark'd