fix: add bounds check for coverage array access

[nh13]

Summary

• Add bounds validation before accessing coverage array
• Prevent potential out-of-bounds memory access

Background

From code review (research.md §1.2, MEDIUM severity):
If graph.coder() returns an unexpected value, the coverage array access could be out-of-bounds, causing memory corruption or crash.

Changes

• src/caller.cpp: Add index validation before coverage array access, print warning if invalid

Test plan

• CI workflow passes
• Coverage calculation still works correctly for valid inputs

Closes #23

🤖 Generated with Claude Code

Summary by CodeRabbit

• Bug Fixes
  • Improved robustness of MSA coverage adjustments by adding bounds validation to avoid invalid index updates.
  • Added diagnostic warnings when a coverage calculation would access out-of-range data, aiding troubleshooting and data integrity.

_{✏️ Tip: You can customize this high-level summary in your review settings.}

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📝 Walkthrough

Walkthrough

Bounds checking added to the pairwise MSA coverage update in src/caller.cpp. The loop index uses size_t, the coverage index is computed into idx and validated against coverage.size() before decrementing; out-of-range indices emit a stderr warning.

Changes

Cohort / File(s)	Summary
Bounds check for coverage array access src/caller.cpp	Loop index changed from int to size_t. Coverage index computed as idx = code * consensus.size() + i and validated (if (idx < coverage.size())) before decrement; emits stderr warning when out of range.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

"I nibble bytes and check each hop,
an index safe, no memory drop.
If idx strays beyond the line,
a warning chirps — all stays fine.
— a careful rabbit 🐇"

Pre-merge checks and finishing touches

❌ Failed checks (1 warning, 1 inconclusive)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	You can run @coderabbitai generate docstrings to improve docstring coverage.
Linked Issues check	❓ Inconclusive	The pull request implements bounds validation for coverage array access and emits warnings for invalid indices, meeting the core requirements [#23]. However, test cases for edge cases are not apparent from the changeset summary.	Confirm whether unit tests covering edge cases for coverage array calculation were added, as required by issue #23.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The pull request title accurately describes the main change: adding bounds check for coverage array access, which is the primary objective of the changeset.
Out of Scope Changes check	✅ Passed	All changes are scoped to the coverage bounds check implementation in src/caller.cpp, with no unrelated modifications detected.

✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix/23-coverage-bounds-check

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📜 Recent review details

Configuration used: defaults

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 31af6cb and 7dbb95d.

📒 Files selected for processing (1)

• src/caller.cpp

🚧 Files skipped from review as they are similar to previous changes (1)

• src/caller.cpp

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[nh13]

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Actionable comments posted: 1

📜 Review details

Configuration used: defaults

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 8eca760 and 31af6cb.

📒 Files selected for processing (1)

• src/caller.cpp