fix index and remove rdd arguments
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
Create a cache for phred -> double values instead of recalculating

Since a phred score is only a byte in size, we can create a small
cache of values instead of recalculating the probabilities on each
requeest.
add pluginDependency section and remove versions in plugin sections
Merge pull request #66 from heuermh/plugin-dependencies

add pluginDependency section and remove versions in plugin sections
Merge pull request #60 from arahuja/readidx

Bugfix for BQSR: Offset into qualityScore list was wrong
Merge pull request #65 from bigdatagenomics/matt-phredcleanup

Create a cache for phred -> double values instead of recalculating
fix for wildcard exclusion maven warnings
sonatype-nexus-snapshots repository is already in parent oss-parent-7 pom
Merge pull request #67 from heuermh/wildcard-exclusions

fix for wildcard exclusion maven warnings
Merge pull request #68 from heuermh/remove-sonatype-snapshot-repo

sonatype-nexus-snapshots repository is already in parent oss-parent-7 pom
Change RecalTable to use optimized phred calculations
Merge pull request #71 from arahuja/usephred

Change RecalTable to use optimized phred calculations
Added ability to create regions from reads, and to merge adjacent regions.
Merge pull request #72 from bigdatagenomics/read-to-reference-region

Added ability to create regions from reads, and to merge adjacent regions
Add support for loading/combining multiple ADAM files into a single RDD.

A new method, AdamContext.loadAdamFromPaths, loads a set of ADAMRecord files separately and then returns the union -- it should handle the case where the different files have different sequence dictionaries associated with them.

A method, findFiles, recursively searches a path for sub-directories whose names match a given regex.  We (Genome Bridge) are using these methods to load multiple ADAM files, each produced from a separate BAM that came from a single sample (but were separated by chromosome or, more generically, genomic region).

Including ReferenceMapping, and implicit ADAMRecord -> ReferenceMapping conversion.
This is used to generalize the RichRDDReferenceRecords class (renamed from RichADAMRDD, a name which was, as Frank pointed out, ambiguous).
Add a CHANGES file to help track changes for release notes
Merge pull request #73 from genomebridge/recursive-load

Support for loading/combining multiple ADAM files into a single RDD.
Updated CHANGES.txt to include note about the recursive-load branch.