Validate VCF sample options and other CLI args upfront

[tfenne]

Summary

• Validate VCF --sample name exists in the VCF header upfront, before the simulation loop, with an error message that lists available samples
• Validate that multi-sample VCFs require --sample to be specified (and that single-sample VCFs work without it)
• Reject --sample without --vcf
• Reject output prefix when parent directory doesn't exist
• Add write_vcf_header_only() test helper for creating multi-sample VCFs
• Add 6 integration tests covering all validation paths

Test plan

• cargo ci-fmt passes
• cargo ci-lint passes
• cargo ci-test passes (177/177 tests, including 6 new validation tests)

Summary by CodeRabbit

• Bug Fixes
  • Improved validation for --sample and --vcf option combinations with clearer error messages
  • Enhanced error messages to display up to 10 available VCF sample names (previously 5)
  • Added validation to verify the output directory exists before simulation starts
  • Strengthened VCF sample configuration validation at startup

[coderabbitai]

📝 Walkthrough

Walkthrough

The changes add preflight validation to the simulate command, verifying that --sample requires --vcf, validating VCF sample configurations, and checking that the output directory exists. A new VCF validation function is introduced with enhanced error messaging, and comprehensive integration tests are added to verify validation behavior.

Changes

Cohort / File(s)	Summary
Validation Logic src/commands/simulate.rs, src/vcf/mod.rs	Enhanced Simulate::validate to reject --sample without --vcf, validate VCF sample selections via new validate_vcf_sample function, and verify output parent directory exists. Improved error messages in resolve_sample_index to show up to 10 available samples.
Test Infrastructure tests/helpers/mod.rs	Added TestEnv::write_vcf_header_only method to generate minimal VCF files with headers and sample columns for testing.
Test Coverage tests/test_simulate.rs	Added integration tests validating CLI behavior for --sample and --vcf option combinations, sample matching, multi-sample VCF handling, and output directory existence checks.

Sequence Diagram

sequenceDiagram
    participant User as User/CLI
    participant Simulate as Simulate::validate
    participant VCF as vcf::validate_vcf_sample
    participant Output as Output Dir Check

    User->>Simulate: simulate --sample X --vcf file.vcf --output prefix
    Simulate->>Simulate: Check --sample without --vcf
    alt --sample without --vcf
        Simulate-->>User: Error: bail!
    end
    
    Simulate->>VCF: validate_vcf_sample(path, sample_name)
    VCF->>VCF: Open VCF, read header
    VCF->>VCF: resolve_sample_index(sample_name)
    alt Sample not found
        VCF-->>Simulate: Error with available samples
        Simulate-->>User: Error: bail!
    end
    
    Simulate->>Output: Check parent directory exists
    alt Directory missing
        Output-->>Simulate: Error
        Simulate-->>User: Error: bail!
    end
    
    alt All validations pass
        Simulate-->>User: Proceed to run_simulation
    end

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Estimated Code Review Effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

Poem

🐰 A fluffy bunny hops with glee,
Validating VCF samples, one, two, three!
No sample without a VCF in sight,
Output dirs checked—everything's right! ✨
Tests blooming like carrots, orange and bright!

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately and clearly summarizes the main objective of the PR: adding upfront validation for VCF sample options and other CLI arguments before simulation execution.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ 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 tf/validate-vcf-options

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[coderabbitai]

🧹 Nitpick comments (1)

tests/test_simulate.rs (1)

2976-3111: Add /// doc comments to the six new validation tests.

The new test cases are non-trivial and should follow the same doc-comment style used by the surrounding tests for consistency and discoverability.

As per coding guidelines, "Add doc comments on all public and non-trivial private items".

🤖 Prompt for AI Agents

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

In `@tests/test_simulate.rs` around lines 2976 - 3111, Add triple-slash doc
comments (///) above each of the six new tests explaining what the test
validates: place short one-line descriptions above
test_sample_without_vcf_fails, test_wrong_sample_name_fails,
test_multi_sample_vcf_without_sample_flag_fails,
test_single_sample_vcf_without_sample_flag_works,
test_multi_sample_vcf_with_correct_sample_works, and
test_output_directory_does_not_exist_fails that mirror surrounding tests' style
(e.g., "Checks that ... fails/works when ..."), keeping them concise and focused
on the behavior asserted.

🤖 Prompt for all review comments with AI agents

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

Nitpick comments:
In `@tests/test_simulate.rs`:
- Around line 2976-3111: Add triple-slash doc comments (///) above each of the
six new tests explaining what the test validates: place short one-line
descriptions above test_sample_without_vcf_fails, test_wrong_sample_name_fails,
test_multi_sample_vcf_without_sample_flag_fails,
test_single_sample_vcf_without_sample_flag_works,
test_multi_sample_vcf_with_correct_sample_works, and
test_output_directory_does_not_exist_fails that mirror surrounding tests' style
(e.g., "Checks that ... fails/works when ..."), keeping them concise and focused
on the behavior asserted.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 954a622b-5651-49c3-aaef-f4b3f81a3407

📥 Commits

Reviewing files that changed from the base of the PR and between 5f88918 and 0a3f51d.

📒 Files selected for processing (4)

• src/commands/simulate.rs
• src/vcf/mod.rs
• tests/helpers/mod.rs
• tests/test_simulate.rs