v0.7.0

0.7.0

This release expands AVGs annotations, standardizes HMM annotation and filtering across databases, improves HMMsearch reporting and filtering, and adds reproducibility assets for rebuilding reference tables used by CheckAMG.

Major changes include:

• Expansion of the curated annotations used by CheckAMG (AMGs, APGs, AReGs), plus a large expansion of FOAM and KEGG reference annotations.
• Added CAMPER profile HMMs (McGivern et al., 2024) to the CheckAMG database.
• Added reproducibility assets for rebuilding the required tables/files used by CheckAMG in the notebooks folder.
• KEGG AMGs were expanded using BRITE KO classifications (beyond the previous KOs sourced from VIBRANT).
• False-positive filtering is now driven by explicit, standardized and inspected (see make_checkamg_required_tables.ipynb), pre-flagged HMM ID tables (hard/soft and exception categories) instead of only keyword lists.
• Refined terms used to filter false-positives that were either too strict or lenient.
• HMMsearch reporting is more explicit: the pipeline now carries per-hit "kept vs removed" information (and rationale) and writes a best-hit-per-sequence filtered output in addition to the full hit table.
• Default annotation thresholds were updated: --scaling_factor -> 3.0, --bit_score -> 30, --cov_fraction -> 0.30 (and cov_fraction is now HMM profile coverage, not sequence coverage).