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RNA golden tests, pipeline guide, changelog, contributing guide - #26
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…g, contributing guide, issue templates - regression: rna_* / cdna_* cases (-x rna, -x cdna, splice:hq, splice alias, --cs, --MD --eqx, --junc-bed) on a new synthetic spliced dataset (scripts/make_regression_rna_data.py: 24 genes on both strands, isoforms, micro-exons, a non-canonical intron, a processed pseudogene; direct-RNA-like reads with poly(A) and U, cDNA-like reads with adapters). Same hashes on the AVX2, SSE and scalar paths. - docs/pipelines.md: replacing minimap2 commands, ONT's wf-human-variation with bonefish BAMs, downstream tools, containers. - CHANGELOG.md, CONTRIBUTING.md (build, tests, output-change policy), issue templates. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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rna_*,cdna_*inexpected.tsv) on a new deterministic synthetic dataset: genes on both strands with isoforms, micro-exons, a non-canonical intron and a processed pseudogene; direct-RNA-like reads (poly(A), half with U) and cDNA-like reads (adapters, both orientations). Hashes identical on AVX2, SSE and scalar paths. DNA hashes unchanged.🤖 Generated with Claude Code