fix: filter for hemizygous frequencies does not work (#2100) #2101
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deps-report 🔍Commit scanned: bfd68bf Vulnerable dependencies4 dependencies have vulnerabilities 😱
Outdated dependencies60 outdated dependencies found (including 22 outdated major versions)😢
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🧹 Outside diff range and nitpick comments (2)
backend/variants/query_schemas.py (2)
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450-453: Fix incorrect sample comparison in error handling.There's a bug in the sample comparison logic. The condition is comparing
case_sampleswithquality_samplesagain instead ofgenotype_samples, which could lead to incorrect error reporting.Apply this fix:
- if case_samples != quality_samples: + if case_samples != genotype_samples: raise ValueError( f"Case and genotype samples are not equal: {case_samples} vs {genotype_samples}" )
Line range hint
444-453: Consider refactoring sample validation logic.The sample validation logic is duplicated and could be extracted into a helper method to improve maintainability and reduce the chance of errors like the one found above.
Consider refactoring like this:
+ def _validate_samples(self, case_samples: set, target_samples: set, sample_type: str) -> None: + if case_samples != target_samples: + raise ValueError( + f"Case and {sample_type} samples are not equal: {case_samples} vs {target_samples}" + ) + # In the convert method: - if case_samples != quality_samples: - raise ValueError( - f"Case and quality samples are not equal: {case_samples} vs {quality_samples}" - ) - if case_samples != genotype_samples: - raise ValueError( - f"Case and genotype samples are not equal: {case_samples} vs {genotype_samples}" - ) + self._validate_samples(case_samples, quality_samples, "quality") + self._validate_samples(case_samples, genotype_samples, "genotype")
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backend/variants/query_schemas.py(1 hunks)backend/variants/tests/data/query_settings.py(1 hunks)
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backend/variants/tests/data/query_settings.py
2-2: SyntaxError: Simple statements must be separated by newlines or semicolons
3-3: SyntaxError: Simple statements must be separated by newlines or semicolons
🔇 Additional comments (1)
backend/variants/query_schemas.py (1)
317-317: LGTM: Hemizygous frequency fields added consistently.
The new hemizygous frequency fields have been added following the same pattern as the existing heterozygous and homozygous fields, maintaining consistency across all database types (ExAC, Thousand Genomes, gnomAD exomes, and gnomAD genomes).
Also applies to: 322-322, 327-327, 332-332
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #2101 +/- ##
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Coverage 91% 91%
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Files 678 678
Lines 38537 38537
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Hits 35140 35140
Misses 3397 3397
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