v.1.6.6: GFF-Adder - tool fallback, multi-add supp, strict frame-matching

This minor release focuses on GFF-Adder, which 'adds' additional functionality and error (and IO) handling.

• Fall back to plain GFF parsing when a tool adapter is missing or fails; preserve and record the user-provided -at name.
• Allow a single -at to be applied to multiple -add files (convenience); require 1:1 pairing otherwise.
• Require same 6-frame match for attaching additional annotations to reference features (strict frame matching).
• Clean and standardise 9th-column attributes: explicit ID=Original_Annotation / ID=Additional_Annotation, Tool=, Ref_attrs=, Matched_Tools=, Matched_Annotations=, plus Matched_pct_ref and Pred_len_pct_ref when coords available.
• Add --meta option to write a separate metadata report with detailed matched-pair metrics.
• Ensure output filename ends with .gff if not provided; add helpful verbose warnings when falling back.
• Add plain-GFF parser helper and preserve numeric provenance (tool, info, start, stop) for metric reporting.

Full Changelog: v1.6.5...v1.6.6

v1.5.1: Updated multi-contig handling and output.

v1.5.1: Updated multi-contig handling and output.

Full Changelog: v1.5.0...v1.5.1

v1.5.0: Major update - overhaul of contig handling and improved output

This major update is the first step towards ORForise to handle contigs directly and produce more interpretable outputs.

• Adds an overall summary file with aggregated metrics
• Generates a separate directory for each contig containing:
  • Contig-specific metrics
  • FASTA files for each prediction category (e.g., perfect_matches, undetected_genes)

These changes aim to make downstream analysis easier and results clearer.

Full Changelog: v1.4.2...v1.5.0

v1.4.2: Added Test_Data and added support for genome-wrapped genes.

• Added Test_Data with some example data - Will continue to add more
• Fixed crashes for genes which wrap around the genome - Thanks @Matt-Schmitz #9
• Removed some unhelpful printouts for verbose mode

Full Changelog: v1.4.1...v1.4.2

v1.4.1: Bug fix

This minor release is a bugfix that stops predicted ORFs from being counted as matched if they are double or more the length of their 'matched' gene.

Thanks to @deprekate for the issue raised for this bug (#15 (comment)).

v1.4.0: Bug fixes, optimisation and new features

First thank you to Matt Schmitz (https://github.com/Matt-Schmitz) for identifying a major inefficiency in the overlap checking and providing a detailed fix (See - #11 (comment)). This has provided a significant speedup for comparing annotations (Annotation-Compare and Aggregate-Compare).

GFF_Adder is currently undergoing a major rewrite and should be used with that in mind. The user options and general utility of the tool will change significantly over the next few months.
There was a bug in GFF_Adder which would sometimes mean that overlapping annotations would not be filtered out correctly.
GFF_Adder now has additional functionality which will be documented in the near future.

v1.2.2: Reworked menu system, code optimisation and bug fixes.

v1.2.2: Reworked menu system, code optimisation and bug fixes - Including import issues

ORForise v1.2.1: Package structure corrected to pypi standard

ORForise sub-packages can now be called directly as 'Annotation-Compare' instead of 'python3 -m ORForise.Annotation_Compare'.

Fixed issue where out of order reference GFF file caused crashes.

Fixed issue where out of order reference GFF file caused crashes.
Reference CDSs are now ordered for their start and stop positions before comparisons are made.

This release is the same as ORForise-1.1.2

Corrected: Additional Tool - Balrog

• Fixed minor git issue
• Added consistency of short-output to `Aggregate_Compare.py'