docs(multiplex-quant): document --sample-bc-ori CLI override#200
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an-altosian wants to merge 5 commits into
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docs(multiplex-quant): document --sample-bc-ori CLI override#200an-altosian wants to merge 5 commits into
an-altosian wants to merge 5 commits into
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Add coverage for the new `--sample-bc-ori {fw,rev}` flag introduced in the
companion PR COMBINE-lab#199 against `main`:
- Insert the option in the `simpleaf multiplex-quant -h` snippet.
- Add a "Sample barcode orientation" bullet under Resource resolution
explaining the precedence (CLI > preset > alevin-fry default) and the
fw/rev → forward/reverse translation.
- Add an Examples entry showing a 10x Flex v2 Configuration B run.
Refs: COMBINE-lab#198, COMBINE-lab#199
The published RTD docs were stuck at 0.19.0 in the page title. Bumps conf.py:release to match Cargo.toml (0.25.0). While in the file, address several long-standing gaps in flex-quant-command.rst's `-h` snippet (and its surrounding prose) that accumulated between 0.19.0 and 0.25.0: - Add missing CLI flags to the help snippet: --geometry, --dict, --sample-correction-mode. - Move --sample-bc-list from "Probe Set Options" to "Reference Options" to match the actual help_heading in the source. - Carve --resolution out into a dedicated "Quantification Options" section, matching its help_heading. - Soften the Overview "needs" list to reflect that --chemistry is now optional when --geometry + --cell-bc-list are supplied (cycle-plan variants like 10x Flex Configuration B). - Rewrite the intro paragraph to call out the chemistry-vs-manual-override modes explicitly. Refs: COMBINE-lab#199 (--sample-bc-ori companion code PR)
Explain what fields a chemistry preset stores (geometry, expected_ori, cell BC whitelist, sample BC list + orientation, organism-keyed probe sets, internal version/meta) and how each maps to a CLI override flag. Document how --chemistry and --organism together locate a Flex configuration, and the edge cases where one or both can be omitted. Confirms exhaustively that every behavioral preset field is exposed as a CLI override; only `version` and `meta` are internal-only.
Add a dedicated "Running without --chemistry" section that enumerates the flags that become required when no preset is supplied (each with its source-level bail message), the flags that fall back to defaults, and a worked example showing a full manual configuration for a chemistry not yet in the registry. Source-grounded against multiplex_quant.rs at: L277 (--geometry), L329 (--cell-bc-list), L577 (--probe-set or --index), L749 (--sample-bc-list).
…here Per design discussion on PR COMBINE-lab#199: keep the CLI vocabulary consistent with the chemistry preset JSON and with alevin-fry's --sample-bc-ori. Update the -h snippet, "Chemistry preset structure" bullet, "Sample barcode orientation" prose, and both example commands.
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Summary
Adds documentation for the new
--sample-bc-ori {fw,rev}CLI flag introduced by companion PR #199 (which targetsmain).Why target
dev?ReadTheDocs builds the simpleaf docs from the
devbranch, so doc updates land here. The behavior PR (#199) lands onmain; this PR keeps the published docs in sync once that's merged.Changes
--sample-bc-oriin thesimpleaf multiplex-quant -hsnippet under the main Options section, matching the existing formatting style.fw/rev→forward/reversetranslation that happens before forwarding to alevin-fry.--geometry.Test plan
Refs
main)