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Changelog

All notable changes to bsaseq will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

Added

  • MkDocs Material documentation site (docs/, mkdocs.yml) with a GitHub Pages deploy workflow.
  • CITATION.cff with full author list.

Changed

  • Updated author/maintainer metadata, project URLs, and Docker image (arnstrm2/bsaseq).
  • Condensed CONTRIBUTING.md and the Bioconda recipe README.

Removed

  • paper/ manuscript sources (maintained separately as the manuscript).

1.0.0 - 2025-01-XX

Added

Core Analysis

  • Sliding window analysis with configurable window and step sizes
  • Tricube-weighted smoothing for delta allele frequency
  • G-statistic calculation for each window
  • Z-score normalization for genome-wide significance testing
  • Candidate region detection with automatic merging of adjacent peaks
  • Candidate variant filtering for recessive and dominant inheritance modes

Multi-sample Support

  • Pool multiple samples per bulk (e.g., technical replicates)
  • Weighted allele frequency calculation across pooled samples
  • Sample name validation and overlap detection

Visualization

  • Publication-quality genome-wide Manhattan plots
  • Regional zoom plots for candidate intervals
  • Diagnostic plots for allele frequency and depth distributions
  • Support for PNG and PDF output formats
  • Customizable z-threshold highlighting

Annotation

  • Optional snpEff integration for variant effect prediction
  • Gene-level candidate ranking based on impact and position
  • Annotated candidates output with effect predictions
  • check-snpeff command for installation verification

Input/Output

  • VCF input with automatic format validation
  • TSV output for variants, windows, regions, and candidates
  • BED output for candidate regions
  • Comprehensive analysis summary reports

CLI Features

  • Intuitive command-line interface with Click
  • Rich progress bars and formatted output
  • Comprehensive help text with examples
  • Input validation with helpful error messages
  • samples command for listing VCF sample names
  • plot command for regenerating plots
  • annotate command for standalone annotation

Packaging & Deployment

  • PyPI package with hatchling build system
  • Docker container with optional snpEff
  • Bioconda recipe for conda installation
  • Nextflow pipeline wrapper
  • Snakemake pipeline wrapper
  • GitHub Actions CI/CD pipeline

Dependencies

  • Python 3.9-3.13
  • cyvcf2 >= 0.30.0
  • numpy >= 1.21.0
  • pandas >= 1.4.0
  • scipy >= 1.7.0
  • matplotlib >= 3.5.0
  • click >= 8.0.0
  • rich >= 12.0.0

Documentation

  • Comprehensive README with methodology and examples
  • CLI help text with usage examples
  • Nextflow and Snakemake workflow documentation
  • Contributing guidelines

Version History

Pre-release Development

v0.5.0 - Annotation Integration

  • Added snpEff annotation support
  • Gene-level candidate ranking
  • Annotated output files

v0.4.0 - Visualization

  • Publication-quality plotting
  • Genome-wide Manhattan plots
  • Regional zoom plots
  • Diagnostic plots

v0.3.0 - Candidate Detection

  • Candidate region identification
  • Variant filtering by inheritance mode
  • Region merging algorithm

v0.2.0 - Multi-sample Support

  • Multiple samples per bulk
  • Pooled allele frequency calculation
  • Sliding window analysis

v0.1.0 - Initial Development

  • Basic VCF parsing
  • Variant data models
  • CLI skeleton