Version 1.1.0

Adds:

• --version flag
• Default values are included in the --help output for options.

Fixes:

• Rare problem encountered where read lengths were over 65,535 - internally, read length and related variables are now typed as UInt32 rather than UInt16.
• Refactored code in the determine_actions function to be more readable and to avoid intermittent errors with typing.