Cleaned up system and have compiling now. Depends on adam install from chartl/adam/master.
Cleaned up code. Simple SNP caller has been completed and has documentation added.
Bringing readme documentation up to date.
Moving some code around to clean up. Added file for implementing SNP calls off of data from dbSNP.
Update README.md
Added code to enable packaging Avocado as a single jar without dependencies.
Adding two missing files for SBT.
Fixes to avocado for building a standalone JAR.
Cleaning up for new changes to ADAM format and processing steps.
Adding in read processing stage using ADAM processing pipeline stages.
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.