refactor(correct): eliminate RecordBuf duplication via raw-byte processing

[nh13]

Summary

• Convert execute_single_thread_mode from RecordBuf + TemplateIterator to raw RawRecord reading with manual QNAME grouping, using extract_and_validate_template_umi_raw and apply_correction_to_raw
• Remove the dead RecordBuf else-branch from the batch pipeline process_fn (raw-byte mode is already enabled at pipeline config)
• Simplify CorrectProcessedBatch and CollectedCorrectMetrics by removing Vec<RecordBuf> fields
• Delete extract_and_validate_template_umi (RecordBuf variant), apply_correction_to_record, and their 10 unit tests
• Add characterization test verifying single-thread mode correctness (UMI correction + OX tag)

Net: -222 lines (276 added, 498 removed)

Test Plan

• Characterization test test_single_thread_mode_produces_correct_output passes
• All 2204 unit tests pass
• All 140 integration tests pass
• cargo ci-fmt and cargo ci-lint clean

[codecov]

Codecov Report

❌ Patch coverage is 96.79487% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.27%. Comparing base (ea6e3fc) to head (801dd18).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
src/commands/correct.rs	96.79%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #229      +/-   ##
==========================================
+ Coverage   88.18%   88.27%   +0.09%     
==========================================
  Files         113      113              
  Lines       53388    53215     -173     
==========================================
- Hits        47080    46977     -103     
+ Misses       6308     6238      -70     

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[coderabbitai]

📝 Walkthrough

Walkthrough

The BAM correction pipeline in src/commands/correct.rs migrated from RecordBuf-based processing to raw-byte handling. Changes include removing kept_records/rejected_records vectors from CorrectProcessedBatch, eliminating RecordBuf UMI extraction and correction functions, and updating both multi-threaded and single-threaded execution paths to operate exclusively on raw-byte blocks. The single-threaded path was rewritten to use create_raw_bam_reader and stream records directly. Serialization now handles only raw-byte BAM blocks, and the pipeline signature was simplified to ignore the header argument. Tests were adjusted accordingly with new characterization coverage.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	Title clearly and concisely describes the main refactoring: eliminating RecordBuf duplication by switching to raw-byte processing, which matches the changeset's core objective.
Description check	✅ Passed	Description directly addresses the changeset, detailing the conversion from RecordBuf to raw-byte processing, removed functions, simplified structures, and test coverage.
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/correct-extract-dedup

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[coderabbitai]

🧹 Nitpick comments (1)

src/commands/correct.rs (1)

838-844: unwrap_or_default() silently drops records if template isn't raw-byte mode.

The debug_assert! only fires in debug builds. In release, a misconfigured pipeline would silently lose records. Using .expect() provides fail-fast behavior.

Proposed fix

-                    let raw_records = template.into_raw_records().unwrap_or_default();
+                    let raw_records = template.into_raw_records().expect(
+                        "Template should be in raw-byte mode; RecordBuf mode is no longer supported"
+                    );

🤖 Prompt for AI Agents

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

In `@src/commands/correct.rs` around lines 838 - 844, The code currently calls
template.into_raw_records().unwrap_or_default() after a debug_assert!, which in
release builds will silently drop records; change this to a fail-fast call
(e.g., use expect or unwrap with a clear message) so misconfigured templates
cannot lose data silently: replace the unwrap_or_default() call on
template.into_raw_records() with expect("expected raw-byte mode template:
into_raw_records returned None") (or similar) and keep the debug_assert as-is;
this affects the block around template, into_raw_records, unwrap_or_default and
the subsequent call to Self::extract_and_validate_template_umi_raw so the
failure surfaces immediately with a descriptive message.

🤖 Prompt for all review comments with AI agents

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

Nitpick comments:
In `@src/commands/correct.rs`:
- Around line 838-844: The code currently calls
template.into_raw_records().unwrap_or_default() after a debug_assert!, which in
release builds will silently drop records; change this to a fail-fast call
(e.g., use expect or unwrap with a clear message) so misconfigured templates
cannot lose data silently: replace the unwrap_or_default() call on
template.into_raw_records() with expect("expected raw-byte mode template:
into_raw_records returned None") (or similar) and keep the debug_assert as-is;
this affects the block around template, into_raw_records, unwrap_or_default and
the subsequent call to Self::extract_and_validate_template_umi_raw so the
failure surfaces immediately with a descriptive message.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 5d35da37-2d1e-483b-868a-06a4a3c2c874

📥 Commits

Reviewing files that changed from the base of the PR and between 1ab1bd5 and 801dd18.

📒 Files selected for processing (1)

• src/commands/correct.rs