Unmapped read test

- Unmapped reads should be properly handled when loading from sequence dictionary
Handle unmapped reads

- Unmapped reads should not try to go into the sequence dictionary to
  get their information, nor even set their reference id/name
Add unit tests for marking duplicates

Intellij reports the following coverages now:
Class, %         Method, %       Line, %
100% (23/ 23)    94.4% (34/ 36)  94.8% (55/ 58)
Merge pull request #26 from genomebridge/carlyeks/fixUnmappedReadsInSequenceDictionary

Fix unmapped reads in sequence dictionary
Merge pull request #24 from bigdatagenomics/matt-markduptest

Add unit tests for marking duplicates
Fix build warnings

- Make future build warnings fatal, so that we can address them earlier
Merge pull request #28 from genomebridge/carlyeks/buildWarnings

Fix build warnings
Suppress parquet logging in FieldEnumerationSuite
Merge pull request #30 from genomebridge/carlyeks/suppressLogging

Suppress parquet logging in FieldEnumerationSuite
Fixing a few issues in the ADAM2VCF2ADAM pipeline.
Merge pull request #31 from bigdatagenomics/g2v-hotfix

Fixing a few issues in the ADAM2VCF2ADAM pipeline.
Update POM to support Sonatype OSS deployment
Update the Jenkins script to match POM changes
Remove the GPG Maven plugin

We can sign our artifacts manually instead. This plugin appears to
require users to sign artifacts to even install ADAM in their local
Maven repository.
Reverting cfcdd344a226eb362cf0b036a0fd8854e1be0b6f to fix build for Spark using Hadoop 1.0.4.
Added better debugging output for serialization errors.
GenomicRegionParititioner is a partitioner for ReferencePosition-keyed RDDs.

The GenomicRegionPartitioner divides the total sequence indicated by a SequenceDictionary
into N pieces of equal size, and allows partitioning of RDD[(ReferencePosition, _)] into
region-coherent chunks.
ReferenceRegion represents a contiguous genomic region.

ReferenceRegion is a model representing a contiguous region of a single reference sequence.
I imagine using RR for:
- interval lists representing the target set in exome or gene panel sequencing
- a base for extending to support reference annotations
- binding events in ChIP-seq
- arbitrary "regions of interest" determined as an intermediate result during other calculations.

Anyway, we should have one base model supporting a lot of the common operations of interest
for regions in general.

Added support for Kryo serialization.

Indluded methods for calculating distance and overlap.
Merge branch 'master' of https://github.com/bigdatagenomics/adam