v1.3.4: Some minor changes to UR-Extractor output handling

• Fixed - UR-Extractor now conforms better to 'standard' FASTA and GFF formats.
• Added - 'Multi_Contig_Genome' test directory for testing against fragmented genomes.

v1.3.3: Fixed Con-StORFs middle stop and more IO errors.

• Fixed - Con-StORFs were incorrectly being reported with middle '*' when 'remove_stop' was set to True (default)
• Fixed - In some instances, when using -odir with 'Multiple_Genomes', 'Multiple_Combined_GFFs' or 'Multiple_GFFs', the input directory name was being applied to the output filename.

v1.3.2: Fixed an issue with the hashing of the StORF IDs.

The hashing of StORF IDs may have been different between GFF/DNA and the AA outputs. Now the hashing takes the GFF input filename or in the case of a Pyrodigal run, will take the input FASTA filename.

v1.3.1: Fixed FASTA output and empty dir handling for Multiple_Out_Dirs

Fixes for issues raised in issue: #1

v1.3.0: 'Multiple_Out_Dirs' option added

Small but important release.
StORF-Reporter can now be run on a directory containing multiple Prokka/Bakta output directories.

Example:
StORF-Reporter -anno Prokka Multiple_Out_Dirs -p ../Test_Datasets/Multi_Prokka_Outs

Thanks to @elchaarn (#1 (comment)) for the suggestion.

v1.2.0: Reworked user IO for more user-control and to be OS independent

• Finalised overhaul of user IO to accommodate user requests and become OS independent for StORF-Reporter.
  • Fixed some issues with StORF-Reporter running on a directory of matched Prokka/Bakta gff/fna files.
  • Added option "-af" to allow Prokka/Bakta directory names to differ from internal filename prefixes.
  • Minor changes to parameter handling to ensure "-sout" is called when "-aa" is selected.
  • Feature_Types parameter "-gene_ident Prokka" will select features present in Prokka annotations.

Thanks to @Dx-wmc (#2 (comment)) for suggesting some changes to how StORF-Reporter handles IO.

v1.1.4: Fixed output IDs for Con-StORFs

Pushed missing config changes for v.1.1.4

v1.1.3: Fixed output format for StORF-Extractor

Fixed output format of StORF-Extractor to be more consistent with StORF-Reporter/Finder.

v1.1.2: Fixed a number of output bugs and reworked/simplified some code.

Thanks to @pthieringer for reporting a bug with ('-aa True') outputting the amino acid sequences of the StORFs identified via StORF-Reporter under certain conditions.

Bug link: #3 (comment)

v1.1.1: API handle changed to reflect Pyrodigal update

Thanks to @lobrien20 for identifying the change made by the pyrodigal team to their API call (OrfFinder to GeneFinder).