dentist.commands.maskRepetitiveRegions

This is the maskRepetitiveRegions command of dentist.

Members

Aliases

Options alias Options = OptionsFor!(DentistCommand.maskRepetitiveRegions): Options for the collectPileUps command.

Classes

BadAlignmentCoverageAssessor class BadAlignmentCoverageAssessor: Mask reference regions where the alignment coverage is not within set limits. This helps to identify repetitive or bad quality regions.
RepeatMaskAssessor class RepeatMaskAssessor: This class comprises the collectPileUps step of the dentist algorithm

Functions

assessmentStage MaskAssessmentStage!Assessor assessmentStage(string name, Assessor assessor, const(AlignmentChain[]) input): Construct a stage of the repeat mask assessment pipeline.
execute void execute(in Options options): Execute the collectPileUps command with options.

Interfaces

RepeatAssessor interface RepeatAssessor: A RepeatAssessor should generate a repeat mask derived from a set of alignment chains.

Meta

Source

See Source File

License

Subject to the terms of the MIT license, as written in the included LICENSE file.

Copyright

© 2018 Arne Ludwig <arne.ludwig@posteo.de>

Authors

Arne Ludwig <arne.ludwig@posteo.de>

dentist commands modules