Add Scalariform settings to pom
Check in the scalariform formatted source
Change from deprecated manifest erasure to runtimeClass
Fix Scalariform issues and Maven warnings

We had some Unicode characters in our comments which were causing
Scalariform to throw an exception during processing.  Also, Maven
requires an empty "relativePath" attribute in the parent POM, otherwise
it was trying to resolve parent artifacts in some invalid location.
Remove Scalariform from process-sources phase
Add special id to plugin execution

This special ID tells Maven to use this configuration when running from
the command line.
Update jenkins-test to run scalariform
Change from ClassManifest to ClassTag
Remove shadowing import
Move Hadoop methods into utility class
fasta contig search bugfix; fasta converter refactor; split to functions;
Upgrade to Spark 0.9.1
Update CHANGES.md in prep for release
[maven-release-plugin] prepare release adam-parent-0.9.0
[maven-release-plugin] prepare for next development iteration
BQSR cleanups and fixes
Add BQSR debug flags
Remove attempted emulation of GATK 1.6
style and naming fixes
Add CycleCovariate