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.
Merge pull request #18 from bigdatagenomics/0.7.0-rc3

Reupgraded to Spark 0.9.0. Added config for assembler.
Added a filter that filters genotypes that have been called with a high strand bias.
Merge pull request #17 from bigdatagenomics/basic-filters

Added a filter that filters genotypes that have been called with a high strand bias.
Issue #19 Change references from ADAMFastaNucleotideContig to ADAMNucleotideContig
Merge pull request #20 from arahuja/removefasta

Issue #19 Change references from ADAMFastaNucleotideContig to ADAMNucleo...