Removed extra command 'BuildInformation' from ADAMMain
Merge pull request #266 from karenfeng/command-cleanup

Removed extra command 'BuildInformation'
ADAMFlatGenotype is a smaller, flat, simpler version of a genotype schema.

Also:
1. Added support for missing genotypes in the VCFLineConverter for
   ADAMFlatGenotype.
2. Added a ReferenceMapping for the ADAMFlatGenotype
3. the flat genotype converter uses multiple writers for smaller output
   files.
4. Don't ignore VCF files in .gitignore
Merge pull request #259 from genomebridge/flat-genotype-rebased

ADAMFlatGenotype is a smaller, flat version of a genotype schema
Utility classes for Parquet reimplementation in Scala.

The following changes were made as part of this commit:

* Added a dependency on the AWS Java SDK.

This dependency is listed as 'provided', because the AWS SDK for Java adds 8k+ classes,
which pushes our uber-jar over the standard 65k file limit in the Zip archive.

* Added ByteAccess trait and implementations.

ByteAccess is a trait representing "sources of bytes" for which random access is available,
e.g. local files, S3, etc. This is going to be used to wrap different data storage back-ends,
for raw byte access and allowing us to go around the hadoop library itself.

* Added SerializableAWSCredentials is an AWSCredentials which is Serializable.

We're going to need to pass around (serializable) credentials for S3, in order to
implement our ParquetRDD that reads directly from S3.

* Added CredentialsProperties encapsulates reading AWS credentials from configuration.

This is a wrapper class, designed to allow us to recognize and retrieve credentials from
the environment, config files, or other sources.

* Added FileLocator and implementations.

FileLocator, and its implementations, are a common wrapper around local Files, classpath locations,
bucket/keyname pairs in S3, and static byte arrays (for testing).  This is a way (also serializable)
for naming the location of parquet files and indices in different systems.
Merge pull request #264 from genomebridge/parquet-utils-rebase

Parquet-related Utility Classes
Updating CHANGES.md for the 0.12.0 release
[maven-release-plugin] prepare release adam-parent-0.12.0
[maven-release-plugin] prepare for next development iteration
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