General cleanup to remove cruft from merging code.
Rearranging project structure to match with package naming.
Merge pull request #8 from bigdatagenomics/cleanup

General cleanup to remove cruft from merging code.
Adding tests to pileup callers and read callers.
Also, refactoring variant callers to minimize repeated code and to unify code style with code style from the ADAM project.
Reorganized project to break sufficient statistics components into seperate database oriented view.
Refactoring main avocado body to better enable complex partitioning, and pipeline generation from a config file.
Merge pull request #10 from bigdatagenomics/cleanup-0.0.2

Cleanup 0.0.2
Adding support in for new FASTA contig class in ADAM.
Merge pull request #11 from bigdatagenomics/new-adam-fasta

Adding support in for new FASTA contig class in ADAM.
Adding optimized DefaultPartitionSet, better documentation, and tests.
Merge pull request #12 from bigdatagenomics/default-partitioner

Adding optimized DefaultPartitionSet, better documentation, and tests.
Working pipeline. Added simple first cut configuration file. Resolved bugs with configuration system.
Merge pull request #13 from bigdatagenomics/working-pipeline

Working pipeline. Added simple first cut configuration file.
Adding indel realigner to pipeline.
Merge pull request #14 from bigdatagenomics/indel-realigner

Adding indel realigner to pipeline.
Upgraded avocado to spark 0.9.0 and scala 2.10.3. On the way, fixed a few small bugs.
Merge pull request #15 from bigdatagenomics/small-fixes

Upgraded avocado to spark 0.9.0 and scala 2.10.3.
Revert "Upgraded avocado to spark 0.9.0 and scala 2.10.3. On the way, fixed a few small bugs."

This reverts commit d311aac8210c67d439ca7413226dfd98397d5873.
Merge pull request #16 from bigdatagenomics/revert-spark-0.9

Reverts upgrade to spark 0.9.0
Reupgraded to Spark 0.9.0. Added config for assembler.