filter alignments if using --vcf-samples

[pdimens]

fixes #285
fixes #287

Summary by CodeRabbit

• Bug Fixes
  • Phasing and imputation workflows now consistently restrict alignment inputs to the samples selected from the VCF when sample filtering is enabled.
  • Improved sample matching helps prevent unrelated alignment data from being included in processing.
• New Features
  • Added support for retrieving sample names directly from VCF files, improving sample selection and validation.

[coderabbitai]

📝 Walkthrough

Walkthrough

The --vcf-samples option now filters alignment inputs for impute and both phase subcommands. VCF.samplelist() exposes header sample names, and XAM.filter() retains matching BAM/SAM files. An unused local variable was removed.

Changes

VCF sample filtering

Layer / File(s)	Summary
Sample discovery and alignment filtering harpy/validation/vcf.py, harpy/validation/xam.py	Adds VCF header sample extraction and in-place filtering of alignment files by sample basename; removes an unused local variable.
Command workflow filtering harpy/commands/impute.py, harpy/commands/phase.py	Impute and the bam and snp phase subcommands filter alignments to the matched VCF samples when vcf_samples is enabled.

Estimated code review effort: 2 (Simple) | ~10 minutes

Sequence Diagram(s)

sequenceDiagram
  participant ImputeOrPhaseCommand
  participant VCF
  participant XAM
  participant Workflow
  ImputeOrPhaseCommand->>VCF: Match configured samples
  VCF-->>ImputeOrPhaseCommand: Return selected sample names
  ImputeOrPhaseCommand->>XAM: Filter alignment files
  XAM-->>Workflow: Provide filtered alignments

Loading

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Out of Scope Changes check	⚠️ Warning	The PR also changes phase.py to filter alignments in phasing commands, which is outside the linked impute-only issue.	Move the phase.py update to a separate PR or link an issue for it, and keep this change focused on impute plus its helpers.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	The changes implement the requested --vcf-samples restriction for the STITCH run in impute, matching the linked issue.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly describes the main change: filtering alignments when --vcf-samples is used.

✨ 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 typer

---

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.}

[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@harpy/validation/xam.py`:
- Around line 157-164: Update the alignment filtering flow in filter() so
self.lr_type and self.count are recomputed from the retained self.files after
keeplist filtering. Ensure both phase workflows use this refreshed metadata when
deciding linked-read processing, including when all linked-read BAMs are
excluded.

🪄 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: Repository UI

Review profile: CHILL

Plan: Pro

Run ID: 781be5fc-108b-4a51-92fe-2d18a202f5aa

📥 Commits

Reviewing files that changed from the base of the PR and between 620f46f and a7c312e.

📒 Files selected for processing (4)

• harpy/commands/impute.py
• harpy/commands/phase.py
• harpy/validation/vcf.py
• harpy/validation/xam.py