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.
Adding fixed depth prefix trie implementation, as part of read error correction work.
Merge pull request #268 from fnothaft/prefix-trie

Adding fixed depth prefix trie implementation
Use maven license plugin to ensure source has correct license
Merge pull request #278 from massie/license

Use maven license plugin to ensure source has correct license
Added an ExportFastq command.

ExportFastq takes an ADAM / BAM / SAM file as input, and produces a collection of fastq files
for the single-ended and paired-end reads with those file(s).  Depending on the number of partitions,
it may produce multiple fastq files; these can then be concatenated as necessary.
Created Export command, adding ADAM to BAM export.

Wrote an 'unconvert' method in SAMRecordConverter.
Adding TODO comments.
Scalariform-induced syntax and whitespace changes.