GFF4 is a graph-native pangenome annotation toolkit for projecting linear GFF3 gene models onto embedded graph paths, then querying genes, transcripts, exons, CDS, and related features directly by graph coordinates.
The first release focuses only on the coordinate and query core:
- parse GFA1
S,L, andPrecords - build embedded path step indexes
- convert path intervals to graph walks
- import GFF3 features onto graph coordinates
- validate graph walks and feature hierarchy
- query by node, edge, path interval, or gene
- export path-specific GFF3 for round-trip checks
Later releases will add copy/allele modeling, anchors, snarls, PAV/CNV matrices, graph-SV/GWAS annotation, and production storage.
python -m pytestThe initial development target is the hand-checkable toy graph under examples/toy/.