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

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Authors: Nick Dimonaco, Matt-Schmitz, Amanda Clare
Cited by: 0

Abstract

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: https://github.com/NickJD/ORForise/compare/v1.6.5...v1.6.6

Publication details

Journal / source
Zenodo (CERN European Organization for Nuclear Research)
Publication date
12 February 2026