Version 1.1.1
Noteworthy changes:
- Added description of program flow to documentation
- Introduced parameter "enable_raw_alignment" for enabling/disabling raw alignment step
- Renamed output file parameter to "output_name"
- Introduced parameter "output_prefix" for prefixing dataset names in output
- Reworked scheme for input file parameter passing
- Support raw binary data as input files
- Added command line option for version number printing
- Lot of fixes in documentation