v1.3.0

Features

• Decouple report plots (context phylogeny, diversity, allele frequency trajectories, dN/dS, demix, heatmap) from input data and parameterize plot sizes, palettes, and shapes.
• Replace distance calculation Python script with lightweight afwdist for faster allele frequency-weighted distances.
• Upgrade Freyja to v2.0.1 (adds limit solver threads for demixing) and add barcode timestamps to the report.
• Add seed params to IQ-TREE rules for deterministic phylogenetic inference.
• Extract SARS-CoV-2 feature coordinates directly from GenBank and use GenBank qualifiers for annotations.
• Extract and standardize VCF fields and variant annotations using SnpEff/SnpSift.
• Parallelize sample variant processing and filtering and update variant calling thread directives.

Bug fixes

• Correct variant table merging, column names, and duplicates in VCF fields.
• Handle SnpEff error/warning messages correctly and avoid empty columns causing parsing failures.
• Fix dN/dS feature extraction via GenBank file usage.
• Fix plot errors for zero variants or missing data.
• Fix context phylogeny legend and class rendering issues.
• Adjust variant calling and demixing CPU settings to prevent unexpectedly high usage.
• Correct input/output paths, sample name detection, and minor typos.

Documentation and code formatting

• Document SnpEff config fields and new GB_FEATURES key (moves feature lists from JSON to config YAML file).
• Update report CSS and switch font to Noto Sans.
• Clarify input descriptions and add short tl;dr instructions.
• Run Quarto from the command line with updated environment handling.
• Remove unused dependencies and scripts and reduce unnecessary R tidyverse package loading.
• Standardize rule naming and results column types.
• Minor wording and format improvements.

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Full Changelog: v1.2.2...v1.3.0