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.
Fix transform -sort_reads partitioning. Add -coalesce option to transform.

Previously, all unmappped reads when sorting had their referenceId set to
Int.MaxValue. This worked to place unmapped reads at the end of the file
but it also caused all unmapped reads to be placed in a single partition
causing shuffle skew. Unmapped reads are now placed in a range of positions
to distribute them more evenly.
Merge pull request #17 from bigdatagenomics/matt-sortfix

Fix transform -sort_reads partitioning. Add -coalesce option to transform.
Allow the Hadoop version to be specified
Merge pull request #19 from bigdatagenomics/hadoopfix

Allow the Hadoop version to be specified
Added Apache License 2.0 boilerplate to tops of all the GB-copyright files.
Merge pull request #20 from genomebridge/tdanford/licenses

Added Apache License 2.0 boilerplate to tops of all the GB-(c) files