Version 2.2.1

[2.2.1] - 23-09-2026

Added

• Module: plot-imputed-hvcf accepts optional --imputed-bed and --reference-bed inputs alongside hVCF files.
• Plotting: BED tracks use reference coordinates, preserve empty . regions, and warn when reference BED rows lack genome values.

Changed

• CLI: plot-imputed-hvcf now uses explicit --pangenome-hvcf-folder, --imputed-hvcf, and --reference-hvcf options.

Version 2.2.0

[2.2.0] - 23-09-2026

Added

• CLI: mask-unsure-imputed-haplotypes masks imputed BED haplotypes with insufficient read support and can generate confidence plots.
• Example database: Added a runnable low-read-support masking workflow and generated example outputs.

Fixed

• Packaging: Updated the PEP 621 license declaration so modern setuptools can build the package.

v2.1.1

Changelog

[2.1.0] - 19-05-2026

Added

• CLI: upset-plot command to generate UpSet plots from hapIDranges.tsv.
• Module: core-range-detector now supports output plot formats png, pdf, and svg via -f/--format.

Changed

• README: improved documentation and updated example images for plotting and analysis commands.

[2.1.1] - 20-05-2026

Changed

• Module: haplopainting now supports output plot formats png, pdf, and svg via -f/--format.
• Module: core-range-detector fixed bug

Version 2.0.0

Changelog

[2.0.0] - 19-01-2026

Added

• Created CHANGELOG.md to track version history.
• Core CLI: phgtools now uses cli.py with argument parsing and rich UI.
• UI: Added rich library for beautiful terminal output and help menus.
• CLI: Added --version flag to display package version.
• CLI: Added --check-setup flag to verify all dependencies are installed.
• Module: Added hvcf2bed for converting hVCF files to BED format.
• Module: Added haplopainting for visualizing haplotype blocks.
• Module: Added vcf-distance for calculating and plotting distance matrices (uses g.vcf files, outputs matrix + clustered heatmap with dendrogram).

Changed

• Refactored all scripts to use src layout structure.
• Updated pyproject.toml to replace setup.py.
• Module: check-imputated-haplotype - improved data management, prints summary, calculates % in bp coverage, updated plotting.
• Module: plot-imputed-hvcf - now uses matplotlib instead of pygenometracks (faster and cleaner). Added verbose flag with summary output.
• Module: check-setup - updated to check only required dependencies (removed phg, bcftools, agc, anchorwave, tiledb, perl, pygenometracks).
• Dependencies: Added seaborn to requirements. Removed pygenometracks dependency.
• README: Complete rewrite with updated documentation for all modules.
• EXAMPLE DATABASE: New example database with documentation along all pipeline, creating a PHG database from scratch and to take advantage of the phgtools.

Removed

• Module: plot-pangenome-chromosomes - functionality replaced by haplopainting.
• Dependency: Removed pygenometracks - no longer needed.

Fixed

• Fixed regex matching issue in hvcf2bed regarding duplicate checksums.
• Fixed ImportError issues by standardizing the package structure.

Previous Versions

[1.2.0] - 2025-04-02

Added

• Module: fastaFromKey - extract FASTA sequences from ranges using MD5 keys.
• Module: CheckSetup - validate dependencies and system requirements.
• Module: RangePangenomeEvolution - study range acquisition patterns during genome addition.
• Module: GenomeIntersection - analyze genome intersection metrics and identity percentages.
• Module: CoreRangeDetector - identify and visualize core, unique, and accessory genomic ranges.
• Module: GenomeIntersectionFromMapKmers - process PHGv2 map_kmers output for genome analysis.
• Module: PlotImputedHvcf - create ideogram visualizations of imputed h.VCF files.
• Module: PlotPangenomeChromosomes - visualize pangenome haplotypes across chromosomes.
• Module: CheckHaplotypeAllelesInPangenome - query hapIDranges.tsv files for overlapping genomic ranges.

Version 1.2.0

New function: Genome intersection from map kmers
Updated dependencies (tqdm)

Version 1.1.0

· Added FastaFromKey module and notebook
· Added annotation for the new module
· Added perl as requirement for conda env
· Updated annotation and files for database example guide
· Added version file, and phgtools --version command
· Added a check-setup module
· Minor Readme annotation improvements

Full Changelog: v1.0.0...v1.1.0