Merge branch 'working' into local

Merging in basic wrapper functionality.
Merge branch 'working' into local

Added mutseq and mutfastq functionality.
Merge branch 'working' into local
Added some parser tools for Casava 1.8 format FASTQ files and bedtools coverage histograms.
Updated code structure to match in a more general fashion.
File types now contained within their own sub-modules. Parsers were separated, and class namespace were set up for each file type.
Reduced the complexity of the parser. Just looks for the <int> + <int> fields. Everything else ignored. Seems to vary between versions.
Now includes the entire matched line as a key-value pair with key 'default'