Package org.broadinstitute.hellbender.transformers

Class SimpleRepeatMaskTransformer

java.lang.Object

org.broadinstitute.hellbender.transformers.SimpleRepeatMaskTransformer

All Implemented Interfaces:

Serializable, Function<GATKRead,GATKRead>, UnaryOperator<GATKRead>, ReadTransformer, SerializableFunction<GATKRead,GATKRead>

public final class SimpleRepeatMaskTransformer
extends Object
implements ReadTransformer

Masks read bases with a supra-threshold number of A/T's or G/C's within a given window size.

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
SimpleRepeatMaskTransformer(int threshAT, int threshGC, int windowSize)

Method Summary

Modifier and Type	Method	Description
GATKRead	apply(GATKRead read)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.util.function.Function

andThen, compose

Methods inherited from interface org.broadinstitute.hellbender.transformers.ReadTransformer

andThen, compose

Constructor Details

SimpleRepeatMaskTransformer

public SimpleRepeatMaskTransformer(int threshAT,
 int threshGC,
 int windowSize)

Method Details

apply

public GATKRead apply(GATKRead read)

Specified by:

apply in interface Function<GATKRead,GATKRead>

Specified by:

apply in interface SerializableFunction<GATKRead,GATKRead>