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.
Split the adam-commands module into adam-cli and adam-core

This commit bumps the version to 0.6.0.

The new dependency tree is linear -- 'adam-cli' depends on 'adam-core' depends
on 'adam-format'.

All CLI code is now found exclusively in the adam-cli module. There is no
longer any dependencies in adam-core for command-line parsing, etc.
The AdamMain class has been moved from adam.AdamMain to adam.cli.AdamMain.
The 'commands' package has been renamed to 'cli'.

The CompareAdam code has been split with the back-end code in adam-core and
the cli code in adam-cli.

Only the adam-cli module create a self-executing jar for use on the
commandline.

Aux files like the README and Jenkins tests have been updated.