Update Spark to 0.8.1 and add hadoop2.2 profile
Merge services files when building assembly JAR
Wholeheartedly make Hadoop 2.2.0 the default
Add explicit dependency on scala-library 2.9.3
Merge pull request #53 from jey/hadoop22-fix

Fix Hadoop 2.2.0 support, upgrade to Spark 0.8.1
[maven-release-plugin] prepare release adam-parent-0.6.0
[maven-release-plugin] prepare for next development iteration
Adding Yy as base in MdTag
Merge pull request #56 from arahuja/mdtag

Adding Yy as base in MdTag
Adding reads to rods transformation.
Merge pull request #36 from bigdatagenomics/reads-to-rods

Adding reads to rods transformation.
Parse read groups and create mapping from bam/sam header
Merge pull request #48 from arahuja/readgroupsmapping

Parse read groups and create mapping from bam/sam header
Add Filter object as wrapper around Projection
Add recordGroupName to field list
Merge pull request #61 from arahuja/addfilter

Filter utility for inverse of Projection
Adding quantitative comparisons to CompareAdam

This is a major update and extension to the "comparison" framework in CompareAdam.

First, an extension to CompareAdam has been created, that allows for interchangeable "generators" of
pairwise read-comparison metrics.  We've added our own implementations of a few basic metrics, found
in GBComparisons [Carl, that probably needs to change its name...], for things like duplicate flags,
position of alignment, base qualities, and map qualities.  These metrics are then aggregated
using an aggregator (of which the HistogramAggregator is the prominent example at the moment).

CompareAdam now runs a set of these metrics over the reads from a given pair of files, and writes output
suitable for graphical report generation using the plots.R script.

The code for this traversal-and-metric-generation has been oved to a class in adam-core, called
ComparisonTraversalEngine.

Finally, a new CLI tool has been added, "find_reads", supported by the class FindReads.  The find_reads
command is written to facilitate diagnostics on ADAM files which differ in one or more metrics.  It takes a
pair of ADAM files, the names of one or more generators, and filter expressions on each of those generators,
and produces the set of read names from the pair of files whose generated metric values fall within the
corresponding filters.
Add repartition support for ADAM Files