Start Project
Created docs and removed file foo
Set up gitignore and basic workspace configuration using config.sh
Set up gitignore and basic workspace configuration using config.sh
Added config.sh and bash_fnc.sh, as well as some dummy scripts
Restructured workspace to allow modules
Added modules
Working on unit tests for the python library
Set up unit testing for python library methods and classes, and finished filesys.py and seq.py.  Also, fastq_stats.py is working properly
Deleted some placeholder files
Finished wrapper for cutadapt.  Still need to test on real data
Finished wrapper for cutadapt.  Still need to test on real data
Finished wrapper for bwa aln and picard sortsam
added test file
Deleted test file balh
Updated Req.Specs.odt and added Introduction.odp presentation
Updated documentation
Created some scripts in the align and seq modules
Created req.specs as a text file
Created req.specs as a text file