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v1.4.0 (20/05/2026)

  • Better error handling with more diverse error handling classes.
  • Reading reference name from GFA header in gfa2rgfa.
  • Standardising contig names in SN tags to <sample name>#<haplotype name>#<contig name> in gfa2rgfa output.
  • Coordinate conversion with incomplete rGFA (not all nodes have rGFA tags) in view. Not yet implemented for other subcommands.
  • Restructured and improved pytest testing.
  • Better handling of non-linear components in order_gfa, like circular components.

v1.3.2 (25/03/2026)

  • Updated realign to support reads in FASTA/FASTQ, including gzipped inputs by adding the pyfastx dependency to the project.

v1.3.1 (27/01/2026)

  • Fixed issue with inclusion of terminal bubbles on components for proper tagging in order_gfa.
  • Added more checks for GAF file formats in subcommands realign and sort.

v1.3.0 (06/11/2025)

  • Minor updates to find_path for improved error handling when given paths are invalid.
  • Fixed timer issue in gfa2rgfa subcommand. Now reports more accurate time.
  • Minor fixes to gfa2rgfa regarding parsing of S lines and handling of temporary files.
  • Major addition to order_gfa subcommand to allow handling of branched graphs. Now users can provide --ignore-branching flag to create a ordering even when the graph has a branched structure.
  • Addition of --output-scaffold flag in order_gfa subcommand to output the scaffold graph in GFA format. This graph has bubbles collapsed into single nodes to better visualise the scaffold structure.

v1.2.1 (08/09/2025)

  • Updated gaftools gfa2rgfa subcommand to no longer require seqfile by default. The default behaviour is to use the order of assemblies as given in the GFA file.
  • Fixing the time logger issue with gaftools realign subcommand.
  • Bug fix in the index file created by gaftools sort subcommand. The index file was incorrectly skipping the first alignment record.
  • Minor updates to documentation regarding seqfile in gaftools gfa2rgfa subcommand.

v1.2.0 (03/07/2025)

  • Version push intended for manuscript revision submission.
  • Minor updates to documentation includes better explanation of sort and view index structure, and minor error handling changes to order_gfa.
  • Better error handling regarding the --chromosome-order option in order_gfa.
  • Fixed error in sort index creation when sorted GAF file is directed to standard output.

v1.1.3 (30/05/2025)

  • Minor updates to documentation.
  • Due to the CI/CD issues, this version just consists of minor documentation changes which were implemented in the previous version (v1.1.2). Due to PyPI restrictions regarding version names, the documentation are being released as a new version release.

v1.1.2 (30/05/2025)

  • Better BGZF compatibility for all subcommands.
  • Formatting updates with logger.
  • :issue:`34`: Added subcommand gfa2rgfa to convert GFA to rGFA format. Tested with HPRC Minigraph-Cactus Graph (v1.1).
  • Updated documentation to include gfa2rgfa subcommand.
  • Fixing :issue:`38` regarding GitHub CI/CD (that is why this version's date has been changed to 30/05/2025).
  • Updating python requirement to >=3.9 and adding SPDX expression for MIT license.

v1.1.1 (23/01/2025)

  • Updated documentation to include conda installation instructions.
  • Updated documentation to include preprint link and citation text.
  • :issue:`33`: Fixed error when viewing regions spanning multiple nodes.
  • :issue:`32`: Fixed error when trying to extract whole chromosomes.

v1.1.0 (09/10/2024)

  • Adding find_path subcommand to take node path information as input and outputting the sequences.
  • Updated order_gfa subcommand to output chromosome-wise graphs only with --by-chrom flag.
  • Bug fix in view subcommand and minor changes to make it faster.
  • Updated documentation.

v1.0.0 (24/06/2024)

  • Initial commit.