Found during the generalization audit (#125). #125 covers the cosmetic docs scrub; these are cases where the docs make a claim that is wrong or unusable, not merely tRNA-flavored.
1. CCAGGC is presented as a default motif — there is no default
src/leech/cli.py:116 is default=None, but CCAGGC appears as though it were a default in docs/getting-started/quick-start.md:37,48, docs/data_preparation.md:26,71,87, docs/reference/cli.md:92, dev-notes/architecture.md:229,263, and — worst — docs/troubleshooting.md:26 as a copy-pasteable diagnostic (grep -c CCAGGC reference.fa). A reader cannot distinguish it from a --pod5-style placeholder.
Fix: neutral placeholder (--motif YOURMOTIF) on generic pages; keep CCAGGC only in tRNA example material.
2. --feature-start orientation is defined in tRNA anatomy
docs/reference/cli.md:47-48 (repeated at docs/data_preparation.md:194-197): "negative = toward tRNA body / positive = toward adaptor". A user with any other library cannot interpret the flag at all.
Fix: "negative = upstream (5′ of focus base), positive = downstream", with the tRNA reading as a parenthetical.
3. Two pages give contradictory tuning advice
docs/grid-search/grid-search-usage.md:8-10 — "Asymmetric contexts often perform best (e.g. 9500 left / 500 right)"docs/guides/dwell-features.md:114-117 — "the landscape is often flat (less than 2% difference between reasonable window sizes)"
The 9500/500 number's provenance is dev-notes/grid-search-methodology.md:52, where it is qualified "for Phe-Tyr". The qualifier was dropped on the way into the user-facing page, turning one dataset's result into a general recommendation.
Fix: requalify or drop the specific numbers; reconcile the two pages.
4. Broken links
docs/grid-search/grid-search-usage.md:248 and :295 both reference grid-search.md. docs/grid-search/ contains only grid-search-usage.md.
5. The most generic page is not in the nav
docs/remora_comparison.md has zero domain-specific content and is not listed in zensical.toml:13-43, so the one page that reads as task-neutral is the one users never reach. Consider adding it.
6. Contradictory output-format documentation
docs/api/inference.md:40 documents the aa tag as "amino acid label"; docs/getting-started/quick-start.md:142 promises "modification probability tags". Same tool, two different output contracts. Resolution depends on #125 decision 3.
Found during the generalization audit (#125). #125 covers the cosmetic docs scrub; these are cases where the docs make a claim that is wrong or unusable, not merely tRNA-flavored.
1.
CCAGGCis presented as a default motif — there is no defaultsrc/leech/cli.py:116isdefault=None, butCCAGGCappears as though it were a default indocs/getting-started/quick-start.md:37,48,docs/data_preparation.md:26,71,87,docs/reference/cli.md:92,dev-notes/architecture.md:229,263, and — worst —docs/troubleshooting.md:26as a copy-pasteable diagnostic (grep -c CCAGGC reference.fa). A reader cannot distinguish it from a--pod5-style placeholder.Fix: neutral placeholder (
--motif YOURMOTIF) on generic pages; keepCCAGGConly in tRNA example material.2.
--feature-startorientation is defined in tRNA anatomydocs/reference/cli.md:47-48(repeated atdocs/data_preparation.md:194-197): "negative = toward tRNA body / positive = toward adaptor". A user with any other library cannot interpret the flag at all.Fix: "negative = upstream (5′ of focus base), positive = downstream", with the tRNA reading as a parenthetical.
3. Two pages give contradictory tuning advice
docs/grid-search/grid-search-usage.md:8-10— "Asymmetric contexts often perform best (e.g. 9500 left / 500 right)"docs/guides/dwell-features.md:114-117— "the landscape is often flat (less than 2% difference between reasonable window sizes)"The 9500/500 number's provenance is
dev-notes/grid-search-methodology.md:52, where it is qualified "for Phe-Tyr". The qualifier was dropped on the way into the user-facing page, turning one dataset's result into a general recommendation.Fix: requalify or drop the specific numbers; reconcile the two pages.
4. Broken links
docs/grid-search/grid-search-usage.md:248and:295both referencegrid-search.md.docs/grid-search/contains onlygrid-search-usage.md.5. The most generic page is not in the nav
docs/remora_comparison.mdhas zero domain-specific content and is not listed inzensical.toml:13-43, so the one page that reads as task-neutral is the one users never reach. Consider adding it.6. Contradictory output-format documentation
docs/api/inference.md:40documents theaatag as "amino acid label";docs/getting-started/quick-start.md:142promises "modification probability tags". Same tool, two different output contracts. Resolution depends on #125 decision 3.