refactor(raw-bam): deduplicate aux iteration, use field accessors

[nh13]

Summary

Seven simplification fixes reducing code by ~208 lines:

• Consolidate base decode tables: Remove duplicate BASE_DECODE and DECODE constants, use single BAM_BASE_TO_ASCII everywhere
• Deduplicate find_mc_tag: Rewrite as one-liner delegating to find_string_tag instead of duplicating the aux iteration loop
• Use aux_data_slice in find_*_in_record: Replace manual offset computation in find_mc_tag_in_record and find_mi_tag_in_record
• Use fields.rs accessors in sort.rs: Replace inline byte operations with named accessor functions (ref_id, pos, flags, read_name, etc.)
• Unify compute_bases_past/before_ref_pos: Extract RefPosMode enum and shared compute_read_pos_at_ref implementation, eliminating copy-pasted overlap logic
• Remove redundant assert + expect in builder.rs: Direct cast after length guard
• Consolidate test aux-finders: Replace 143 lines of duplicated test helpers with 3-line delegations to production tags.rs functions

Test plan

• cargo nextest run -p fgumi-raw-bam — all tests pass
• cargo clippy -p fgumi-raw-bam --all-features -- -D warnings — no warnings
• cargo check (full workspace) — clean
• cargo ci-fmt — clean

[coderabbitai]

📝 Walkthrough

Walkthrough

This pull request refactors field access patterns across the BAM record handling crate by consolidating field extraction into helper functions, reducing code duplication, and removing redundant decoding tables. Changes include replacing manual byte offset calculations in sort.rs and tags.rs with accessor calls, removing BASE_DECODE in favor of existing BAM_BASE_TO_ASCII, introducing a RefPosMode enum for cleaner position calculation logic, and adjusting a u8 cast in builder.rs. Comprehensive unit test coverage is added across multiple modules (cigar.rs, fields.rs, sequence.rs, tags.rs) to exercise existing functionality. Public API signatures remain unchanged.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description check	✅ Passed	Description clearly outlines all seven simplifications with specific examples matching the changeset across all modified files.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.
Title check	✅ Passed	The title accurately describes the main objectives of the changeset: deduplicating aux iteration and consolidating field accessor usage throughout the crate.

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✨ Finishing Touches

• 📝 Generate docstrings (stacked PR)
• 📝 Generate docstrings (commit on current branch)

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch refactor/nh/simplify-fgumi-raw-bam

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 83.49%. Comparing base (fa96485) to head (2ad9de6).
⚠️ Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #135      +/-   ##
==========================================
- Coverage   83.50%   83.49%   -0.01%     
==========================================
  Files         126      126              
  Lines       51375    51375              
==========================================
- Hits        42901    42898       -3     
- Misses       8474     8477       +3     

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[coderabbitai]

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 `@crates/fgumi-raw-bam/src/cigar.rs`:
- Around line 868-990: Several test functions in this module have duplicate
names and will fail compilation (E0428); locate the duplicated test functions
named test_query_length_from_cigar_empty,
test_read_pos_at_ref_pos_raw_before_alignment,
test_read_pos_at_ref_pos_raw_in_deletion,
test_read_pos_at_ref_pos_raw_with_insertion, and
test_read_pos_at_ref_pos_raw_with_soft_clip and either remove the redundant
copies or rename them to unique identifiers (e.g., append _2 or a descriptive
suffix) so each test function name is unique; ensure any renamed tests keep the
same assertions and references to helper functions like query_length_from_cigar
and read_pos_at_ref_pos_raw.

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ℹ️ Review info

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 0488610 and 1a35942.

📒 Files selected for processing (8)

• crates/fgumi-raw-bam/src/builder.rs
• crates/fgumi-raw-bam/src/cigar.rs
• crates/fgumi-raw-bam/src/fields.rs
• crates/fgumi-raw-bam/src/overlap.rs
• crates/fgumi-raw-bam/src/sequence.rs
• crates/fgumi-raw-bam/src/sort.rs
• crates/fgumi-raw-bam/src/tags.rs
• crates/fgumi-raw-bam/src/testutil.rs