Accept yes/no/y/n/t/f as boolean flag values

[nh13]

Summary

• Adds a custom parse_bool value parser in common.rs that accepts true/false/yes/no/y/n/t/f (case-insensitive), matching sopt/fgbio boolean flag behavior
• Wires value_parser = parse_bool into all boolean CLI flags across 17 files
• Adds the full num_args = 0..=1 / default_missing_value = "true" / ArgAction::Set pattern to 17 flags that were still using clap's default SetTrue action (simulate, group, correct, sort, compare, and hidden scheduler flags)
• Every boolean flag in the CLI now consistently supports: --flag (bare), --flag true/false, --flag yes/no, --flag=t/f, etc.

Test plan

• Unit tests for parse_bool: 23 valid cases (all accepted values in various casings), 13 invalid cases (typos, nonsense, whitespace)
• Integration tests for extended values through clap: 10 valid CLI cases, 5 invalid CLI cases
• All existing boolean flag parsing tests continue to pass
• Full test suite: 2283 tests pass, 0 failures
• cargo ci-fmt and cargo ci-lint clean

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 88.98%. Comparing base (7c1cc80) to head (1d36434).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #235   +/-   ##
=======================================
  Coverage   88.97%   88.98%           
=======================================
  Files         113      113           
  Lines       55038    55065   +27     
=======================================
+ Hits        48970    48998   +28     
+ Misses       6068     6067    -1     

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[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 4a13c38d-d6b7-4a41-92ff-13da42742a62

📥 Commits

Reviewing files that changed from the base of the PR and between 9dc160d and 1d36434.

📒 Files selected for processing (17)

• src/commands/clip.rs
• src/commands/common.rs
• src/commands/compare/bams.rs
• src/commands/compare/metrics.rs
• src/commands/correct.rs
• src/commands/dedup.rs
• src/commands/downsample.rs
• src/commands/duplex_metrics.rs
• src/commands/fastq.rs
• src/commands/filter.rs
• src/commands/group.rs
• src/commands/review.rs
• src/commands/simulate/consensus_reads.rs
• src/commands/simulate/fastq_reads.rs
• src/commands/simulate/grouped_reads.rs
• src/commands/sort.rs
• src/commands/zipper.rs

✅ Files skipped from review due to trivial changes (1)

• src/commands/filter.rs

🚧 Files skipped from review as they are similar to previous changes (9)

• src/commands/review.rs
• src/commands/clip.rs
• src/commands/compare/bams.rs
• src/commands/simulate/grouped_reads.rs
• src/commands/zipper.rs
• src/commands/compare/metrics.rs
• src/commands/correct.rs
• src/commands/common.rs
• src/commands/group.rs

---

📝 Walkthrough

Walkthrough

Added pub(crate) fn parse_bool(s: &str) -> Result<bool, String> in src/commands/common.rs for case-insensitive boolean parsing (true/false, t/f, yes/no, y/n) and extended unit tests. Updated many CLI boolean flags across command modules to use value_parser = parse_bool and, where applicable, to allow optional values (num_args = 0..=1, default_missing_value = "true", ArgAction::Set). In sort removed some clap conflicts_with rules and introduced runtime checks plus tests that error when conflicting flags are used.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	Title clearly describes the main change: adding support for additional boolean flag value formats (yes/no/y/n/t/f) alongside true/false.
Description check	✅ Passed	Description is directly related to the changeset, detailing the parse_bool implementation, affected files, test coverage, and expected behavior.
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 nh13/feat-parse-bool

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

src/commands/common.rs (1)

628-634: Consider making parse_bool crate-private.

This reads like an internal clap helper. If external crates are not meant to call it, pub(crate) keeps the public API surface smaller.

🤖 Prompt for AI Agents

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

In `@src/commands/common.rs` around lines 628 - 634, The parse_bool helper is
currently exported publicly but intended as an internal clap helper; change its
visibility from pub to pub(crate) on the function declaration for parse_bool to
keep it crate-private, and update any internal references if necessary (search
for parse_bool usages) to ensure they remain in-crate; no other behavioral
changes are needed.

🤖 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/commands/sort.rs`:
- Around line 172-173: Remove the attribute-level conflicts on the verify flag
(the conflicts_with settings on the verify field which, combined with
ArgAction::Set, treat --verify=false as "present") and instead add runtime
validation in the command's execute() method: check if self.verify is true and
if so bail with clear errors when self.output.is_some() or self.write_index is
true (e.g., "--verify cannot be used with --output" and "--write-index cannot be
used with --verify"). Ensure the checks reference the verify field, output
option and write_index flag and run before proceeding with the rest of
execute().

---

Nitpick comments:
In `@src/commands/common.rs`:
- Around line 628-634: The parse_bool helper is currently exported publicly but
intended as an internal clap helper; change its visibility from pub to
pub(crate) on the function declaration for parse_bool to keep it crate-private,
and update any internal references if necessary (search for parse_bool usages)
to ensure they remain in-crate; no other behavioral changes are needed.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 3a25df5d-ff43-4b82-90eb-37edf063b47f

📥 Commits

Reviewing files that changed from the base of the PR and between 7c1cc80 and 9dc160d.

📒 Files selected for processing (17)

• src/commands/clip.rs
• src/commands/common.rs
• src/commands/compare/bams.rs
• src/commands/compare/metrics.rs
• src/commands/correct.rs
• src/commands/dedup.rs
• src/commands/downsample.rs
• src/commands/duplex_metrics.rs
• src/commands/fastq.rs
• src/commands/filter.rs
• src/commands/group.rs
• src/commands/review.rs
• src/commands/simulate/consensus_reads.rs
• src/commands/simulate/fastq_reads.rs
• src/commands/simulate/grouped_reads.rs
• src/commands/sort.rs
• src/commands/zipper.rs