Modified to allow VCF input containing MAFs for more advanced calling
Merge pull request #1 from bigdatagenomics/maf-call

Modified to allow VCF input containing MAFs for more advanced calling
Adding read filtering. Cleaning up main read processing pipeline.
Merge pull request #2 from bigdatagenomics/avocado-cleanup-main

Adding read filtering.
Cleaning up with new ADAMRod. Should improve performance by eliminating repeated groupBys for pileups.
Merge pull request #5 from bigdatagenomics/pileups-to-rods

Cleaning up with new ADAMRod.
EMforAlleles contains two main methods: emForMAFs and emForAFS. Used for multisample calling.
Adding on multiple sample SNP calling algorithm.
Merge pull request #3 from bigdatagenomics/maf-call

EMforAlleles contains two main methods: emForMAFs and emForAFS.
Added kmer graph assembly and pairwise alignment HMM. Regions must be filtered as active w.r.t. the corresponding reference subsequence. Emits ADAMVariant and ADAMGenotype from called haplotypes.
Merge pull request #4 from bigdatagenomics/assembly

Calling variants from local assembly
Updating with new variant/genotype implementations from Adam PR #13.
Merge pull request #6 from bigdatagenomics/variant-changes

Updating with new variant/genotype implementations from Adam PR #13.
Converting project over to maven.
Merge pull request #7 from bigdatagenomics/sbt-to-mvn

Converting project over to maven.
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.