Edited to include changes to project name
Added new analyses and improved old ones (some files are mostly duplicates can probably partition this better). Working build file
Added a scripting tool for my pipeline
Bug fixes for the aforementioned script
Added SNP read coverage calculation. Modified CalculateNovelSNPCount to use 1000genomes instead of dbSNP (can be changed with one line)
Skeleton for VCFInputFormat
Completed classes required for VCFInputFormat (probably buggy)
Think I've fixed the VCFRecordReader...
Bug not fixed, FSDataInputStream still behaves unpredictably, but making progress on genome parititioning
More work on Known Genes parsing
More work on Known Genes parsing