Add unit tests for marking duplicates

Intellij reports the following coverages now:
Class, %         Method, %       Line, %
100% (23/ 23)    94.4% (34/ 36)  94.8% (55/ 58)
Merge pull request #24 from bigdatagenomics/matt-markduptest

Add unit tests for marking duplicates
Fix build warnings

- Make future build warnings fatal, so that we can address them earlier
Merge pull request #28 from genomebridge/carlyeks/buildWarnings

Fix build warnings