v2.3.0 - #4
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…qc more interpretable
Adds a README subsection explaining how to build a --literature-csv lookup table for pathogens other than SARS-CoV-2, covering the required gene/mutation columns, gene-name matching against the supplied GFF3 annotation, and pointers to the bundled mock template.
Bacterial references commonly reuse gene names across replicons (e.g. repA on both a chromosome and a plasmid). gene_lengths_from_gff3 and generate_gene_table previously aggregated CDS lengths and mutation counts by gene name alone, so two unrelated genes sharing a name on different contigs had their stats silently summed into one row. - gene_lengths_from_gff3 now tracks CDS lengths per (contig, gene) and only disambiguates the output label, e.g. "repA (chrom1)" vs "repA (plasmid1)", when a name actually collides across contigs. Names confined to a single contig stay unqualified. - generate_gene_table splits colliding gene names by chrom using the results table's own chrom column. - Added ambiguous_gene_names() to flag collisions directly from the annotation, closing an edge case where a colliding gene only has variants on one contig in a given run and would otherwise be dropped when merged against the gene-length scaffold. - No change in output for single-contig references or multi-segment references with uniquely-named segments (e.g. 8-segment influenza). Adds tests/test_annotation_processing.py and three new tests in tests/test_analysis.py covering the single-contig baseline, the colliding-name split, and the ambiguous-genes edge case. Starts CHANGELOG.md to track revision-cycle changes going forward.
…ence labels, primer-bed warning
…ling and duplicate-row plotting, add PAO1 validation scripts, correct README/CHANGELOG
…id numpy 2.5's Python-3.12-only PEP 695 stub syntax
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See CHANGELOG.md for full details.