Storf-reporter

This release includes a number of bug fixes, especially for file IO handling and new sub packages for managing StORFs after they have been extracted and added to a new GFF.

Thanks to elchaarn for identifying a bug in calling StORF-Reporter on multiple Bakta/Prokka GFFs.

Fixed some input/output filename bugs which were causing issues with finding input files or writing out of results - Added a -v option to print version and renamed verbose mode option to -verbose - Fixed the reporting of middle Con-StORF stop codons - GFF filename is now used instead of FASTA to output default outfile names - General improvements

Menu overhaul, new input/output options, new tool - StORF-Extractor to get StORF sequences from an extended genome annotation and general optimisations.

v0.6.1 Fixed import bug and added non-PROKKA gff support to StORF-Reporter (CDS annotation tools such as Prodigal can now be run through StORF-Reporter and new augmented GFFs are created as with PROKKA output).

New:
A new look for the `--help' manual page.
An option to report 'short StORFs' that are under 100nts.
A new filtering option is available to filter out StORFs that do not include at least one of the three canonical start codons ('ATG', 'GTG', 'TTG') - Most useful for short StORF reporting.

Code Optimisation and fixes:
General code optimisations (including the removal of unnecessary sorting of StORFs during the filtering stage).
Bug fixes that include the incorrect filtering of Con-StORFs due to a sequence length bug.
Fixes to the StORF-Reporter PROKKA output to now report the same StORF ID between the GFF and FASTA and to only output the DNA sequences of the PROKKA and StORF genes.

Misc:
StORF-Reporter version now in the header of all GFF files produced.