Save Point: WIP for prephix.py (Python version) and SNPInputReader.py
WIP Savepoint: SNPInputReader.py and prephix.py

Bug fixes and now running but no output yet.
Prephix.py -- Release candidate.
WIP Savepoint: More fixes from regression testing.
WIP: SNPInputReader fixed strain name parsing for NUCMER files.
WIP: prephix.py Fixed ref file write out.
WIP: prephix.py fixed procesing order to match perl version.
WIP: SNPInputReader.py - further optimizations.
WIP: prephix.py - Implemented use of logging module.
WIP: SNPInputReader.py bug fixes.
WIP: More fixes and optimizations.

Dropped SNPDataLine object and used built-in tuples as return values for the
reader iterator value.
v2.5.3 prephix (Perl) release of v3.0 prephix (Python)

2.5.3 - Fix to file close operations to avoid race condition on phenolink export.
3.0 - First release of Python version of prephix.