feat: Add support for CellularBarcode operator

[msto]

Closes #66

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📝 Walkthrough

Walkthrough

The PR adds cellular barcode (C) support across the demux pipeline and upgrades read-structure. Added ReadSet::cellular_barcode_segments(). SampleWriters gains cellular_barcode_writers: Option<Vec<W>> and into_parts() now returns five components. Demux wiring, writer-pool construction, write/close loops, header/write logic, output naming, and metrics/docs were updated to include cellular barcode handling and file suffixes. Public API changes expose the new field and into_parts shape. Tests, examples, and test data were extended to cover cellular barcode extraction and end-to-end flows.

Pre-merge checks and finishing touches

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	Title clearly and specifically describes the main change: adding support for the CellularBarcode operator.
Description check	✅ Passed	Description references issue #66, which maps directly to the PR's objective of adding CellularBarcode operator support.
Linked Issues check	✅ Passed	PR fully implements support for the C operator: ReadSet now has cellular_barcode_segments(), SampleWriters includes cellular_barcode_writers, demuxing logic processes cellular barcode reads, and tests verify the functionality [#66].
Out of Scope Changes check	✅ Passed	Changes are scoped to cellular barcode support: dependency update (read-structure 0.1.0→0.2.0), demux.rs modifications for C operator handling, README updates, and related tests. All changes align with issue #66 objectives.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

✨ Finishing touches

🧪 Generate unit tests (beta)

• [ ] Create PR with unit tests
• [ ] Post copyable unit tests in a comment
• [ ] Commit unit tests in branch ms_66_c-operator

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📥 Commits

Reviewing files that changed from the base of the PR and between 20b1a3b03b64eb7a4ae4c8bbb7531048025796ac and 05a84de902f7eb9ae438c3f57ea4921ca5de5a2b.

📒 Files selected for processing (1)

• README.md (5 hunks)

🔇 Additional comments (1)

README.md (1)

52-107: Documentation updates for C operator look good. Changes correctly add cellular barcode (C) support throughout: operator definitions, extraction descriptions, output file naming conventions, and help text. All references are consistent and accurate.

Also applies to: 136-136

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[msto]

@clintval AFAICT the README is autogenerated from the tool help doc. I've updated the tool docs accordingly.

I did run into one new question - the help mentions storing the sample and molecular barcodes in SAM tags. Is that just a helpful guide for downstream usage, or is there related functionality in this repo to update?

[clintval]

I did run into one new question - the help mentions storing the sample and molecular barcodes in SAM tags. Is that just a helpful guide for downstream usage, or is there related functionality in this repo to update?

I actually think that's a bug in the docs when they were copy-pasted from the Scala implementation of this tool. This tool (fqtk demux) merely writes out a bunch of FASTQs and not a SAM/BAM file. So the last two sentences of this paragraph should probably be deleted entirely:

https://github.com/fulcrumgenomics/fqtk/blob/f74eb6c4939c2db123067e50c7e76c07777ebdc2/src/bin/commands/demux.rs#L514-L519