ALF module
- class ResultALF(variant_flagged: TestOutcomes, info_flag: enum.Flag | None, reads_seen: int, avg_as: float | None)[source]
Bases:
FlagResult- reads_seen: int
- avg_as: float | None
- getinfo(alt: str) str[source]
Return basic filter info in a string formatted for use in the VCF INFO field - “<flag>|<code>”.
Each filter must return INFO as it should be formatted for the VCF INFO field, or None if not applicable. Subclasses must override this method to return more specific info.
- FlagName: ClassVar[str] = 'ALF'
- InfoFlagsAllSet: ClassVar[Flag | None] = 7
- class FixedParamsALF(*, avg_AS_threshold: float)[source]
Bases:
FixedParams- avg_AS_threshold: float
- model_config: ConfigDict = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True}
parent dataclass to be be inherited from to store specific fixed parameters for a particular subclass of FilterTester, or in other words for a particular filtering test. Using subclasses of this class for the fixed parameters provides type-safety and a consistent interface for implementing filters
- test_ALF(run_params: RunParamsShared, fixed_params: FixedParamsALF)[source]
- class FlaggerALF(engine_fixed_params: FixedParams | None, require_marks: Sequence[str], exclude_marks: Sequence[str])[source]
Bases:
ReadAwareProcessAlignment score filter based on AS tag
- AddsMarks: ClassVar[set[str] | None] = None
- EngineFactory() ProcessEngineProtocol[RunParams, FlagResult]
- FixedParamClass
alias of
FixedParamsALF
- ProcessNamespace: ClassVar[str | None] = 'ALF'
- ProcessType: ClassVar[ProcessKindEnum | None] = <class 'hairpin2.infrastructure.process_engines.VariantFlaggerEngine'>