Create README.md

[monica-cheng1]

Greptile Summary

The PR adds a comprehensive README describing the MiXCR Clonotyping block, its configuration, outputs, use cases, operational guidance, licensing, and citations. One UMI configuration statement overstates what supplying a tag pattern alone enables.

• Clonotype — A grouped receptor sequence with quantified abundance; the README introduces the block’s clonotype extraction and downstream usage.
• MiXCR preset — A predefined pipeline configuration for a library chemistry; the README explains preset selection and its role in supplying pipeline defaults.
• Assembling feature — The receptor-region span used to form clonotypes, such as CDR3 or VDJRegion; the README documents available ranges and downstream implications.
• UMI — A unique molecular identifier used to distinguish original molecules from PCR duplicates; the README adds setup and counting guidance, but should clarify that the preset must also declare UMI tags.
• Tag pattern — A MiXCR expression describing barcode and UMI positions in reads; the README introduces it as the mechanism for extracting those tags.
• Primer boundary — The configurable alignment edge associated with primer placement; the README explains its relevance to primer-bounded amplicons.
• Custom reference library — A user-supplied germline reference set; the README documents file-based and MiXCR Library Builder sources.
• Stop-codon replacement — Translation of amber, ochre, or opal codons to configured residues for suppressor-strain libraries; the README documents the feature and its purpose.

Confidence Score: 4/5

The UMI guidance should be corrected before merging because it can cause users to mistake read-based output for molecule-corrected abundance.

The implementation passes custom tag patterns to MiXCR but gates unique-molecule output fields on UMI metadata from the selected preset, while the new README presents the tag pattern alone as sufficient.

Files Needing Attention: README.md

Important Files Changed

Filename	Overview
README.md	Adds user-facing documentation for the block; most claims align with implementation, but the UMI FAQ omits the preset metadata prerequisite for molecule-count outputs.

Prompt To Fix All With AI

### Issue 1
README.md:69
**Tag pattern alone lacks UMI counts**

When a user supplies a UMI tag pattern with a preset that does not declare `umiTags`, the export still omits `uniqueMoleculeCount` and `uniqueMoleculeFraction`, so this guidance can cause read-based abundance to be mistaken for molecule-corrected output.

```suggestion
Select a UMI-aware preset and supply a MiXCR tag pattern describing where the UMI sits in your reads. When the preset declares UMI tags, the output includes unique-molecule counts and fractions rather than only read-based abundances. See the [MiXCR tag pattern reference](https://mixcr.com/mixcr/reference/ref-tag-pattern/).
```

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

_{Reviews (1): Last reviewed commit: "Create README.md" | Re-trigger Greptile}

Greptile also left 1 inline comment on this PR.

[greptile-apps]

Tag pattern alone lacks UMI counts

When a user supplies a UMI tag pattern with a preset that does not declare umiTags, the export still omits uniqueMoleculeCount and uniqueMoleculeFraction, so this guidance can cause read-based abundance to be mistaken for molecule-corrected output.

Suggested change

	Supply a MiXCR tag pattern describing where the UMI sits in your reads. Abundances are then counted per unique molecule instead of per read, which removes amplification bias. See the [MiXCR tag pattern reference](https://mixcr.com/mixcr/reference/ref-tag-pattern/).
	Select a UMI-aware preset and supply a MiXCR tag pattern describing where the UMI sits in your reads. When the preset declares UMI tags, the output includes unique-molecule counts and fractions rather than only read-based abundances. See the [MiXCR tag pattern reference](https://mixcr.com/mixcr/reference/ref-tag-pattern/).

Prompt To Fix With AI

This is a comment left during a code review.
Path: README.md
Line: 69

Comment:
**Tag pattern alone lacks UMI counts**

When a user supplies a UMI tag pattern with a preset that does not declare `umiTags`, the export still omits `uniqueMoleculeCount` and `uniqueMoleculeFraction`, so this guidance can cause read-based abundance to be mistaken for molecule-corrected output.

```suggestion
Select a UMI-aware preset and supply a MiXCR tag pattern describing where the UMI sits in your reads. When the preset declares UMI tags, the output includes unique-molecule counts and fractions rather than only read-based abundances. See the [MiXCR tag pattern reference](https://mixcr.com/mixcr/reference/ref-tag-pattern/).
```

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

Note: If this suggestion doesn't match your team's coding style, reply to this and let me know. I'll remember it for next time!