Enable logging via log4j
Increase throughput of bam2adam by reducing lock contention
Fix scripts/jenkins-test to run under Ubuntu
Merge pull request #15 from jey/tweaks-1

Tweaks 1
Fixing an issue in pileup generation and in the MdTag util. Also, adding test coverage.
Merge pull request #16 from bigdatagenomics/pileup-mdtag-fix

Fixing an issue in pileup generation and in the MdTag util.