refactor(zipper): use RawRecord methods in restore_unconverted_bases_in_raw_record

[nh13]

Summary

Cosmetic refactor of `restore_unconverted_bases_in_raw_record` (added in #274) to use `RawRecord`'s inherent methods instead of `bam_fields::*` free-function calls + `&mut Vec` plumbing. Same behavior, same byte-for-byte output, same 17 tests pass.

Part 1 of 7 in the follow-up series closing #272.

Changes

Signature tightens from `record: &mut Vec` to `rec: &mut RawRecord`, which reads more clearly at the call site. Internal replacements:

• `bam_fields::flags(record)` → `rec.is_unmapped()` / `rec.is_reverse()`
• `bam_fields::ref_id` / `pos` → `rec.ref_id()` / `rec.pos()`
• `bam_fields::find_string_tag_in_record` → `rec.tags().find_string()`
• `bam_fields::get_cigar_ops` → `rec.cigar_ops_vec()`
• `bam_fields::reference_length_from_cigar` → `rec.reference_length()`
• `bam_fields::get_base` / `set_base` → `rec.get_base()` / `rec.set_base()` (seq_offset no longer needed at call site)
• `bam_fields::remove_tag` → `rec.tags_editor().remove()`

The single caller (`restore_unconverted_bases_in_raw_template`) bridges `template.raw_records` (still `Vec<Vec>` in `Template`) by wrapping each entry in `RawRecord::from` via `std::mem::take` and restoring it with `into_inner`.

Test plan

• `cargo ci-test` — 2541/2541 pass
• `cargo ci-fmt` clean
• `cargo ci-lint` clean (clippy pedantic + `-D warnings`)
• All 17 `test_restore_unconverted_bases_*` tests (RecordBuf path + raw-byte path + parsing) pass unchanged

Stack

• PR 1 (this): zipper `restore_unconverted_bases_in_raw_record` → RawRecord methods
• PR 2: fgumi-raw-bam additive API (write helpers, CigarOp/Kind, TagValue, converters, SamBuilder, IndexedRawBamReader, inherent delegators)
• PR 3: fgumi-sam raw helpers + RawRecordClipper
• PR 4: consensus internals → RawRecord + drop RecordBuf variants
• PR 5: commands + storage + pipeline collapses
• PR 6: workspace test migrations to SamBuilder
• PR 7: delete vendored bam_codec + simulate → SamBuilder

[codecov]

Codecov Report

❌ Patch coverage is 84.00000% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.03%. Comparing base (05e89b8) to head (f820ecd).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
src/lib/commands/zipper.rs	84.00%	4 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #286   +/-   ##
=======================================
  Coverage   90.03%   90.03%           
=======================================
  Files         122      122           
  Lines       61791    61813   +22     
=======================================
+ Hits        55632    55652   +20     
- Misses       6159     6161    +2     

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 82044aaa-ece1-4bff-8450-eb79d99ed4af

📥 Commits

Reviewing files that changed from the base of the PR and between 7a3a042 and f820ecd.

📒 Files selected for processing (1)

• src/lib/commands/zipper.rs

📝 Walkthrough

Walkthrough

The methylation restore function in zipper.rs was refactored to use RawRecord from fgumi_raw_bam instead of directly mutating Vec<u8> buffers. Raw BAM byte accessors and helpers were replaced with RawRecord methods for reading/writing bases, checking unmapped/reverse status, looking up tags, and managing CIGAR operations. Tags like NM and MD are conditionally removed only when the sequence is modified. Tests were updated to construct RawRecord instances from encoded bytes and convert back afterward, maintaining byte-level parity in test verification.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	Title clearly and specifically summarizes the main refactoring: replacing bam_fields calls with RawRecord methods in the restore_unconverted_bases_in_raw_record function.
Description check	✅ Passed	Description is directly relevant, detailing the cosmetic refactor with clear mapping of old calls to new RawRecord methods, test results, and context within a larger PR series.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch nh/raw-bam-api-6-zipper-raw-record-methods

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[nh13]

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