First version of Piculus. Lots of work still to be done though.
Updated picard lib stuff
Updated package names
Added code comments for docs in ContigPosition
Added code comments for docs and Java7 updatess in piculus.fasta
Handle situation where number of seqs requested is greater than that available
Added command line help
Created smaller methods from some code used more than once.
Generated javadoc for new methods
Created, implemented and documented the getBadReadsFastqWriter method
Updated methods and tests
Renamed to GenomeHelper
Renamed to GenomeHelper
Edited Main method
Edited Main method and added gitignore for test_out_data
Deleted data in test_data_out
Added dist and build directories to repo
Create README.md
Edited ReadMe
Delete README.md