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… negative strand
Instead of erroring when a GFA input contains no circular sequences, dnaapler now warns, copies the input GFA to the output, and writes all sequences out as a linear FASTA. For `dnaapler all` and `dnaapler bulk`, a reorientation summary is also written with every contig marked No_reorientation. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Adds tests/test_golden.py, which runs representative dnaapler commands and compares their reoriented outputs against committed snapshots in tests/test_data/golden/. Sequences are fingerprinted as length + sha256 (so goldens stay tiny), while small deterministic files (the no-circular summary) are stored verbatim. Covers chromosome/plasmid/phage/archaea (MMseqs2 paths, incl. the no-start-codon overlapping-ORF branch), largest on a negative-strand CDS (guards #102), nearest, mystery (default seed), and GFA input (reorientation + the no-circular passthrough with summary). These run automatically in CI via `pytest tests/`. Regenerate intentionally-changed snapshots with: DNAAPLER_UPDATE_GOLDEN=1 pytest tests/test_golden.py Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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