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.
Changes before merge.
Merge branch 'master' of github.com:bigdatagenomics/avocado into assembly
Working compile with latest adam changes. Simple fix for partitioning reads into fixed size windows.