Martel based parser to read IntelliGenetics formatted files.

This is a huge regular regular expression for IntelliGenetics, built using the regular expressiona on steroids capabilities of Martel.

http://hiv-web.lanl.gov/ALIGN_97/HIV12SIV-index.html

Notes: Just so I remember -- the new end of line syntax is: New regexp syntax - \R \R means "\n|\r\n?" [\R] means "[\n\r]"

This helps us have endlines be consistent across platforms.

out_sequence ( seq )