Write gene_id_to_name.tsv when indexing a probe set CSV#202
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When `simpleaf index` builds from a 10x probe set CSV that carries a gene symbol column (`gene_name` or `gene_symbol`), it now emits a `gene_id_to_name.tsv` mapping into the reference and the built index. Previously this mapping was only produced on the auto-build path inside `multiplex-quant`/`quant` (via probe_utils), so a prebuilt probe index passed with `--index` carried no gene names. The GTF/roers path already wrote the file; this brings the probe-csv path to parity, letting downstream `quant` surface gene names for prebuilt probe indexes. The mapping covers every gene in the probe set independent of the `included` flag (it is a complete gene annotation, not matrix contents); conflicting names for the same gene_id are rejected. The insert-with-conflict-check and TSV-write logic are factored into two shared `probe_utils` helpers (`insert_gene_name`, `write_gene_id_to_name`) used by BOTH the auto-build path and `simpleaf index`, so the logic is not duplicated. Adds a unit test for the dedup/conflict behavior.
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What
simpleaf index --probe-csvnow writes agene_id_to_name.tsvmapping into the reference dir and copies it into the built index, when the probe set CSV carries a gene-symbol column (gene_nameorgene_symbol).Why
The gene_id→name mapping was only generated on the auto-build path used by
multiplex-quant/quant(viaprobe_utils::convert_probe_csv_to_reference_files). When a user prebuilds a probe index withsimpleaf index --probe-csvand passes it via--index, no mapping was produced, so downstreamquantcould only surface Ensembl gene IDs, not names. The GTF/roers reference path already emitsgene_id_to_name.tsv; this brings the probe-CSV path to parity.Behavior
includedflag (a complete gene annotation, not matrix contents).gene_idare rejected with a clear error (matchesprobe_utilssemantics).index_info["gene_id_to_name"]; the existing copy step propagates the file into the final index dir, soquantpicks it up automatically.Tests
insert_gene_name_dedups_and_detects_conflicts(dedup + conflict).simpleaf index --probe-csvon a 3-gene CSV (including an excluded-only gene) producesref/gene_id_to_name.tsvandindex/gene_id_to_name.tsvwith all genes mapped.Scope
Single-file change:
src/simpleaf_commands/indexing.rs.