code cleanup + fix iterators

- fix iterators use in
SequenceFromFiles::generateUserFriendlySequencePattern() (fixes
https://github.com/MrKepzie/SequenceParsing/issues/1 )
- convert many while loops to for loops
- use std::size_t when applicable (and remove many useless casts to int)
- make removeFileExtension() more robust
Merge pull request #2 from devernay/fixiterators

code cleanup + fix iterators