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@jsarriaa jsarriaa released this 19 Jan 12:53
· 23 commits to main since this release
v2.0.0.0
b416e2e

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.
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