organizing into folders. adding small example
converting file read to streaming
fixing ArrayIndexOutOfBoundsException
Removed reading in batches.
adding strong namespace package names back in. removing extra whitespace.
Regenerate PairHM test data for new implementation
Fix the absolute value check on the PairHMM test
Update to latest LoglessPairHMM code

fix GSATDG-99, GSATDG-87, GSATDG-88
Master repo cleanup

The master repo now contains only the original java implementation from the Broad Institute and the final directory structure. All other projects should live in their own branches for now. We should discuss how to integrate them into master once they're stable.
Adding output.txt and test_data to gitignore
Adding propper logging
Adding PairHMM options and simpler test reports
QualityUtils: cleaner and with better docs
Removing the big test file from the repo