docs(zipper): name the tc tag in comments that still say pa

[nh13]

fgumi zipper writes the template-coordinate sort key as tc, and has since 0.2.0, when the tag was renamed to stop colliding with bwa-mem's pa:f (primary-alignment score fraction). The code says so — add_template_coordinate_tags_raw appends SamTag::TC and tc_info_from_raw reads it — but about forty doc comments, inline comments, and assertion messages in zipper.rs still call it the pa tag. The section banner reads "Primary Alignment Tag (pa) Tests", naming the exact tag the rename exists to avoid, and failures print messages like Supplementary should have pa tag for a tag no fgumi release has written in four minor versions.

This renames those to tc, plus the has_pa_tag local. The --skip-pa-tags flag alias is deliberately untouched — that spelling is real and stays accepted.

One site in fgumi-raw-bam keeps its pa literal: test_dedup_pa_tag_check_fails_on_b_array reproduces a historical dedup bug and the legacy bytes are the point. Its comment claimed the tag was "produced by fgumi zipper", which stopped being true in 0.2.0; it now says what it actually is and notes that the tag name is incidental to the bug — what defeats dedup's check is the B:i array type, which tc still uses.

Comments and assertion messages only; no behavior change. Verified to merge cleanly with #682, which touches the help text in the same file.

Summary by CodeRabbit

• Documentation

  • Clarified template-coordinate metadata terminology and legacy tag context.
  • Updated comments and test descriptions to consistently reference the tc tag.

• Tests

  • Improved regression test clarity for template-coordinate tags without changing existing behavior.

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📥 Commits

Reviewing files that changed from the base of the PR and between 565df42 and 86c94f9.

📒 Files selected for processing (2)

• crates/fgumi-raw-bam/src/tags.rs
• src/lib/commands/zipper.rs

---

Walkthrough

The change replaces legacy pa terminology with tc in comments, helper documentation, test descriptions, diagnostics, and assertions. Tag-generation behavior remains unchanged.

Changes

Template-coordinate tag terminology

Layer / File(s)	Summary
Align tc documentation and tests crates/fgumi-raw-bam/src/tags.rs, src/lib/commands/zipper.rs	Comments, helper documentation, test descriptions, diagnostics, and assertions now consistently refer to the tc template-coordinate tag and its B:i representation.

Estimated code review effort: 1 (Trivial) | ~5 minutes

Possibly related PRs

• fulcrumgenomics/fgumi#529: Introduced the tc tag behavior referenced by these documentation and test updates.
• fulcrumgenomics/fgumi#617: Also updates zipper.rs from legacy pa terminology to tc.
• fulcrumgenomics/fgumi#682: Also updates documentation and tests for the historical pa to tc rename.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly identifies the documentation and comment updates that rename the template-coordinate tag from pa to tc.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.95%. Comparing base (565df42) to head (86c94f9).
⚠️ Report is 11 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #695      +/-   ##
==========================================
- Coverage   93.95%   93.95%   -0.01%     
==========================================
  Files         178      178              
  Lines      108059   108059              
==========================================
- Hits       101525   101523       -2     
- Misses       6534     6536       +2     

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