docs: specify order of clipping operations in ClipBam docs

[clintval]

Good idea to document this order (since order does matter) from this issue:

• ClipBam --clip-bases-past-mate ignores 5' hard-clipped bases in mate #1141 (comment)

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between d540c9c and ed4f04c.

📒 Files selected for processing (1)

• src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala

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

• src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala

---

📝 Walkthrough

Walkthrough

This PR adds documentation to the ClipBam tool explaining the sequence of clipping operations. The new paragraph outlines four steps: upgrade clipping, fixed 5' and 3' clippings, overlapping-read clipping, and clipping reads past their mate. The changes are purely documentary—no functional logic or control flow modifications are introduced.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately describes the main change: adding documentation about the order of clipping operations in ClipBam.
Description check	✅ Passed	The description is relevant, referencing the motivating issue and explaining why the documentation change was made.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch cv_specify_order

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

[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 `@src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala`:
- Around line 72-77: Update the clipping-order paragraph wording to use singular
grammar ("The order of operations for clipping is:") and clarify step 4 to state
that clipping bases past the mate applies only to FR pairs; reference the
existing options/flags in the code (--upgrade-clipping,
--clip-overlapping-reads, --clip-bases-past-mate) and the runtime check
(clipBasesPastMate && r1.isFrPair) so the doc text matches the implementation.

---

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 b776c5e and d540c9c.

📒 Files selected for processing (1)

• src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala

[github-actions]

PR Preview Action v1.6.1
🚀 View preview at https://fulcrumgenomics.github.io/fgbio/pr-preview/pr-1143/
Built to branch gh-pages at 2026-03-04 01:52 UTC. Preview will be ready when the GitHub Pages deployment is complete.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.96%. Comparing base (b776c5e) to head (ed4f04c).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1143   +/-   ##
=======================================
  Coverage   95.96%   95.96%           
=======================================
  Files         132      132           
  Lines        8037     8037           
  Branches      516      516           
=======================================
  Hits         7713     7713           
  Misses        324      324           

Flag	Coverage Δ
unittests	95.96% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.