Validate NAIBR BEDPE records before inferring structural-variant classes

[thierrygosselin]

Summary

harpy-utils infer-sv previously assumed that every NAIBR BEDPE record contained the expected number of columns and a valid orientation code. Malformed or changed input could therefore produce an uninformative IndexError or KeyError.

This change validates the input before structural-variant inference:

• reject empty files and headers with too few columns;
• reject malformed records with a line-specific error;
• validate orientation values against the four supported NAIBR mappings;
• preserve the existing handling of passing and FAIL records.

The resulting error messages identify the offending line and value, making upstream-format changes and damaged files much easier to diagnose.

Scope

This is intentionally limited to input validation and diagnostics. It does not change the structural-variant classification rules.

Summary by CodeRabbit

• Bug Fixes
  • Added validation for empty or malformed NAIBR BEDPE input files.
  • Reports clear errors for records with insufficient columns or unsupported orientation values.
  • Preserves meaningful line endings and reports the affected input line during processing.

[coderabbitai]

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Run ID: 8f412780-19cb-49f7-82b2-e5a029de73ad

📥 Commits

Reviewing files that changed from the base of the PR and between a7e3543 and ac1f2e1.

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• harpy/utils/infer_sv.py

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📝 Walkthrough

Walkthrough

infer_sv now validates NAIBR BEDPE headers and records before processing. It reports empty input, short rows, and unsupported orientations with click.ClickException, including the invalid record line number.

Changes

BEDPE input validation

Layer / File(s)	Summary
Input validation and processing harpy/utils/infer_sv.py	The header must contain at least seven columns. Each record must contain at least seven columns and use an orientation present in conversions. Invalid records report their line number. Parsing removes only line endings with rstrip("\r\n").

Priority: ⬇️ Low

Estimated code review effort: 3 (Moderate) | ~15–30 minutes

Merge Risk: ⚪ Minimal · up to ac1f2

The command now rejects malformed NAIBR BEDPE input with specific errors while preserving existing passing, FAIL, and SV classification behavior. No current merge-blocking risk remains.

🚥 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 and concisely describes the main change: validating NAIBR BEDPE records before structural-variant inference.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 1 functions across 1 files.
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.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[pdimens]

Thank you for submitting this PR! I'm in favor of the validation, but I also have to ask about what use-case you have encountered that a malformed BEDPE file would be used as input for the utility? Within harpy, infer-sv exclusively works on the output produced by the sv naibr workflow.

[thierrygosselin]

Thanks Pavel, that makes sense. I mainly had two defensive edge cases in mind:

1. BEDPE files that are truncated or edited during troubleshooting or reruns
2. A future change to the NAIBR BEDPE output format, although unlikely

The validation is intended to give a clear line-specific error in those cases while leaving the normal sv naibr workflow unchanged.

Does that make sense?
Cheers and say Hi to Nina for me
Thierry

[pdimens]

Yeah, that makes sense. Thanks for the helpful contribution!