v1.4.2: Cleaned up some error messages, removed ORForise as a dependancy, fixed -spos parameter and corrected GFF positional information in some situations.

In this minor update:

• ORForise was removed as a dependency as only a single function was being called, which is now being handled internally.
• Some error messages were tweaked for clarity.
• The user option '-spos' which switches StORFs from being reported with or without the first Stop Codon (start position) in the FASTA and GFF files failed on some occasions and is now fixed - This should also offer improved compatibility with tools such as Panaroo that do not like in-frame stop codons.

v1.4.1: Minor bug fixes for 'empty' contig handling and StORF filtering

This minor update includes two fixes

• As highlighted by @LucyDillon in issue #4, StORF-Reporter was falling over when presented with an input contig WITHOUT any previous annotation. This was caused by the fact that CDS etc annotations presented to StORF-Reporter are used as anchors in the 'StORF-Filler' function which fits StORFs in the correct order in the new computed GFF file.
• There was a small issue with how some StORFs were filtered on opposite strands. That is now fixed and should results in less spurious StORFs being reported.

v1.4.0: StORFs now rejected for non-standard NTs & minor bug fixes and speedups

This minor release includes a few niche bug fixes/speedups and one new user option.

• New user option '-non_standard' which by default removes StORFs with more than 20% non-standard nucleotides (X's etc) - this can be helpful when working with 'low-quality' sequencing or assemblies.
• A few small low-hit bugs were identified and fixed. For example, if Pyrodigal 'mode' is run with default parameters on short-sequences, it would fail at the pre-training step as no sequence was >=20kb and some input filename handling was improved.
• For the StORF 'tile filtering', set theory was originally used to check if the smaller StORF was inside or overlapped the larger by more than n nucleotides. While not very impactful timewise, it has now been significantly sped up by just using min/max ranges.

Full Changelog: v1.3.4...v1.4.0

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