Storf-reporter

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.

v.1.4.1
This minor update includes two fixes

- As highlighted by LucyDillon in issue https://github.com/NickJD/StORF-Reporter/issues/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.

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**: https://github.com/NickJD/StORF-Reporter/compare/v1.3.4...v1.4.0

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

* 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.

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.

Fixes for issues raised in issue: https://github.com/NickJD/StORF-Reporter/issues/1