process module

class ReadAwareProcessProtocol(engine_fixed_params: OptFixedParams_T, require_marks: Sequence[str], exclude_marks: Sequence[str])

Bases: Protocol[RunParams_T, OptFixedParams_T, OptEngineResult_T]

ProcessNamespace: ClassVar[str | None]

EngineFactory: ClassVar[Callable[[FixedParams], ProcessEngineProtocol[RunParams, FlagResult | None]] | Callable[[None], ProcessEngineProtocol[RunParams, FlagResult | None]] | None]

ProcessType: ClassVar[ProcessKindEnum | None]

FixedParamClass: ClassVar[type[FixedParams] | None]

AddsMarks: ClassVar[set[str] | None]

property require_marks: set[str]

property exclude_marks: set[str]

property fixed_params: OptFixedParams_T

property run_params: RunParams_T

reset() → None

class ReadAwareProcess(engine_fixed_params: FixedParams | None, require_marks: Sequence[str], exclude_marks: Sequence[str])

Bases: ABC

ProcessNamespace: ClassVar[str | None] = None

EngineFactory: ClassVar[Callable[[FixedParams], ProcessEngineProtocol[RunParams, FlagResult | None]] | Callable[[None], ProcessEngineProtocol[RunParams, FlagResult | None]] | None] = None

ProcessType: ClassVar[ProcessKindEnum | None] = None

FixedParamClass: ClassVar[type[FixedParams] | None]

AddsMarks: ClassVar[set[str] | None] = None

require_properties_check(run_params: RunParams)

Filter reads prior to test

Since marks are based only on presence, the lack of an exclude mark is enough to pass a check. This makes it easy to enable and disable tagger processes while leaving it up to the user which way round they want to use a tag. E.g. if you want to be able to easily turn something on/off, make it an exclude mark like LOW-QUAL conversely if you want to be strict, make a required mark like HIGH-QUAL

property require_marks

property exclude_marks

property fixed_params: FixedParams | None

property run_params: RunParams

prime(var_params: RunParams, overwrite: bool = False)

reset()