Package org.broadinstitute.hellbender.utils.downsampling

package org.broadinstitute.hellbender.utils.downsampling
  • Class
    Description
    AlleleBiasedDownsamplingUtils
    The purpose of this set of utilities is to downsample a set of reads to remove contamination.
    Downsampler<T>
    The basic downsampler API, with no reads-specific operations.
    DownsampleType
    Type of downsampling method to invoke.
    DownsamplingMethod
    Describes the method for downsampling reads at a given locus.
    FractionalDownsampler
    Fractional Downsampler: selects a specified fraction of the reads for inclusion.
    LevelingDownsampler<T extends List<E>,E>
    Leveling Downsampler: Given a set of Lists of arbitrary items and a target size, removes items from the Lists in an even fashion until the total size of all Lists is <= the target size.
    MutectDownsampler
     
    PassThroughDownsampler
    Pass-Through Downsampler: Implementation of the ReadsDownsampler interface that does no downsampling whatsoever, and instead simply "passes-through" all the reads it's given.
    PositionalDownsampler
    PositionalDownsampler: Downsample each stack of reads at each alignment start to a size <= a target coverage using a ReservoirDownsampler.
    ReadsDownsampler
    An extension of the basic downsampler API with reads-specific operations
    ReadsDownsamplingIterator
    Iterator wrapper around our generic {@link ReadsDownsampler)} interface.
    ReservoirDownsampler
    Reservoir Downsampler: Selects n reads out of a stream whose size is not known in advance, with every read in the stream having an equal chance of being selected for inclusion.