Merge pull request #204 from hammerlab/avro-field-visibility

Update Avro code gen to not mark fields as deprecated.
Add Scalariform settings to pom
Merge pull request #206 from hammerlab/scalariform-maven-config

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.
Merge pull request #207 from massie/erasure-cleanup

Change from deprecated manifest erasure to runtimeClass
Merge pull request #209 from hammerlab/maven-warning-and-scalariform-fixes

Fix Scalariform issues and Maven warnings
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