feat: add --includelist option to simulate fastq-reads

[nh13]

Summary

• Adds --includelist / -i option to fgumi simulate fastq-reads that samples UMIs from a whitelist file instead of generating them randomly
• UMI length is inferred from the includelist, overriding --umi-length (with a warning if they differ)
• Validates includelist format: one UMI per line, all same length, ACGT-only, blank lines skipped, lowercase uppercased

This enables generating synthetic FASTQ data that exercises the full correct → extract → ... → consensus pipeline in fgumi-benchmarks, since reads contain UMIs from a known whitelist that fgumi correct can match against.

Test plan

• 7 unit tests for load_includelist (valid, lowercase, blank lines, invalid bases, mismatched lengths, empty file)
• 1 integration test verifying molecule UMIs are sampled exclusively from the includelist
• Manual smoke test: generated 100 molecules with 5-UMI whitelist, verified all truth UMIs are whitelist combinations
• Pre-commit hooks pass (ci-fmt, ci-lint)
• CI

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📒 Files selected for processing (1)

• src/commands/simulate/fastq_reads.rs

---

📝 Walkthrough

Walkthrough

Adds a new CLI option --includelist/-i to provide a file of UMIs and extends GenerationParams with an optional in-memory includelist. Implements load_includelist to read one UMI per non-blank line, trim/uppercase entries, require only A/C/G/T bases, reject empty lists, and enforce uniform UMI length with line-specific errors. When provided, the includelist's length overrides --umi-length; mismatches warn, and UMI length is validated against read length. During molecule generation UMIs are sampled with replacement from the includelist independently for R1 and R2. Unit tests added for parsing, validation, length checks, and generation sourcing.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly and concisely summarizes the main change: adding a --includelist option to the simulate fastq-reads command.
Description check	✅ Passed	The description is directly related to the changeset, providing clear context on the feature, validation rules, test coverage, and motivation.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch nh/simulate-fastq-includelist

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[codecov]

Codecov Report

❌ Patch coverage is 90.73171% with 19 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.00%. Comparing base (7442efd) to head (23dad2a).
⚠️ Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
src/commands/simulate/fastq_reads.rs	90.73%	19 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #198      +/-   ##
==========================================
+ Coverage   86.12%   88.00%   +1.87%     
==========================================
  Files         110      111       +1     
  Lines       51974    52464     +490     
==========================================
+ Hits        44765    46173    +1408     
+ Misses       7209     6291     -918     

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[nh13]

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Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@src/commands/simulate/fastq_reads.rs`:
- Around line 266-278: When overriding umi_length from includelist (the
includelist variable -> list[0].len()), validate that the includelist UMI length
does not exceed the configured read length (e.g., self.common.read_length) and
reject the request if it does: instead of silently overriding and truncating
later, return an error (or bail) with a clear message referencing the
includelist UMI length and read length; update the same validation logic at the
other includelist-handling site around the second occurrence (the block at
~580-587) so both places enforce list[0].len() <= read_length before assigning
umi_length or using the UMI. Ensure you reference the variables includelist,
umi_length, self.common.umi_length, and self.common.read_length when
implementing the check and message.

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---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 7e8cde8d-ac67-435c-8de0-e565b260be94

📥 Commits

Reviewing files that changed from the base of the PR and between 7442efd and 6e250d8.

📒 Files selected for processing (1)

• src/commands/simulate/fastq_reads.rs

[nh13]

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