Changes

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.

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

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.

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.

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.

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.

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.

Better BGZF compatibility for all subcommands.
Formatting updates with logger.
#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 #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.

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.