I am testing gxfkit, a Rust implementation of selected AGAT-compatible GFF/GTF workflows.

The production-supported path is gff2gtf, using AGAT 1.7.0 as the correctness oracle. On the gated core corpus (human_chr1, human_chr21, yeast), the output is 100% normalize-identical after documented order-only normalization.

The current main branch also has a gxf2gxf standardization beta. It is fixture-gated against AGAT and has a public residual ledger, but it is not a full AGAT replacement yet.

I am looking for real GFF3 files that stress AGAT hierarchy standardization: missing parents, direct CDS/exon/UTR children, transposable-element loci, or unusual RefSeq/FlyBase-style structures.

Useful feedback would include:

• AGAT version.
• gxfkit version or commit.
• Original command lines.
• Minimal input snippet if possible.
• The smallest AGAT-vs-gxfkit output difference.

Feedback thread: https://github.com/benngaihk/gxfkit/issues/7

Parity ledgers: https://github.com/benngaihk/gxfkit/blob/main/docs/PARITY.md https://github.com/benngaihk/gxfkit/blob/main/docs/GXF2GXF-PARITY.md