v1.2.0

GVClass v1.2.0

Highlights

• Updated reference database v1.2.0 with refined GA thresholds and model annotations.
• Improved HMM model accuracy through updated gathering thresholds.
• Added functional annotations to HMM models.
• Bug fixes and documentation improvements.

Database updates

• New database tarball: resources_v1_2_0.tar.gz.
• Expanded reference coverage:
  • Nucleocytoviricota and Mirusviricota genomes from Vasquez et al. (2025) bioRxiv.
  • Mirusviricota models and genomes from Medvedeva et al. (2026) Nature Microbiology.
  • Models for Polinton-like viruses (PLV) and virophages (PV) from Roux et al. (2023) Biomolecules.
  • Extended VP, PLV and phage reference set from MetaVR database (Fiamenghi et al. 2025).

New output columns

• VP (Virophage) metrics: vp_completeness, vp_mcp, vp_df.
• PLV metrics: plv.
• Mirus metrics: mirus_completeness, mirus_df.
• NCLDV MCP: ncldv_mcp_total (includes OG1352, OG484).
• Removed old columns mirus_unique, mirus_total, mirus_dup (replaced by completeness metrics).

CLI improvements

• --no-mode-fast renamed to --extended / -e (fast mode remains default).

Bug fixes

• Removed time.sleep() usage in prefect_flow.py.
• Fixed inconsistent bytes encoding in genetic_code_optimizer.py.

Documentation

• Added full CLI reference table and expanded --contigs documentation.
• Documented genetic code selection logic (9 codes tested, selection criteria).
• Mermaid diagram now correctly shows code 0 (meta mode with pretrained models).