BAMpiro 1.0.1

The first consolidated BAMpiro release: a self-contained interactive QC report, alignment-free lineage & drug-resistance typing, a metadata-driven dose-analysis layer, and a full documentation site.

Highlights

• Interactive QC report (bin/qc_report.py) — one self-contained HTML dashboard for the whole cohort (live thresholds & presets, sample-exclusion basket, dark/light theme, mobile-responsive, per-section (i) popovers) plus a machine-readable per-sample qc_flags.tsv. Panels: SNP dynamics, epistasis, SNP matrix, drug resistance, lineage summary, distributions, correlations / QC-space PCA, genome landscape, functional annotation, gene burden, taxonomic composition (Kraken2), and aDNA damage.
• Alignment-free lineage & drug-resistance typing with Pathotypr (--run_pathotypr), run from the container — reference-agnostic k-mer typing (nested sub-lineage + WHO drug-resistance). Optional dual amino-acid numbering (used reference + canonical H37Rv / Mycobrowser).
• Metadata cohort filter & dose analyses — categorical samplesheet columns (e.g. treatment) drive a report-wide cohort filter; a numeric dose column becomes a first-class metric and powers a Dose × treatment Kruskal–Wallis test and a Variant × dose allele-frequency-vs-dose Spearman scan with Benjamini–Hochberg FDR.
• Documentation — a MkDocs Material site with a guided Tutorials series (first run → samplesheet → configuration → reading the report → typing → phylogeny → longitudinal analysis → non-TB organism), a runnable Jupyter notebook, and a live example QC report.
• Pipeline — length-aware genmap mappability read masking, virgin + masked consensus, CRAM output (--output_cram), selectable publish mode, and optional region-parallel FreeBayes.

Full detail in the CHANGELOG.

1.0.0

First release version of BAMpiro with the complete pipeline