Change from ClassManifest to ClassTag
Remove shadowing import
Move Hadoop methods into utility class
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
Merge pull request #210 from hammerlab/maven-warning-and-scalariform-fixes

Remove Scalariform from process-sources phase
Merge pull request #212 from massie/warning-cleanup

Cleanup build warnings
fasta contig search bugfix; fasta converter refactor; split to functions;
Merge pull request #211 from hammerlab/fasta-refactor

FastaConverter Refactor
BQSR cleanups and fixes
Add BQSR debug flags
Remove attempted emulation of GATK 1.6
style and naming fixes
Add CycleCovariate
remove tabs in pom.xml