Package org.broadinstitute.hellbender.transformers

Class DUSTReadTransformer

java.lang.Object

org.broadinstitute.hellbender.transformers.DUSTReadTransformer

All Implemented Interfaces:

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

public class DUSTReadTransformer
extends Object
implements ReadTransformer

Masks read bases and base qualities using the symmetric DUST algorithm

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final long	serialVersionUID

Constructor Summary

Constructors

Constructor	Description
DUSTReadTransformer(int dust_mask, int dust_w, double dust_t)

Method Summary

Modifier and Type	Method	Description
GATKRead	apply(GATKRead read)
static Collection<scala.Tuple2<Integer,Integer>>	sDUST(GATKRead read, int window, double tscore)	Wrapper method for runDUST so that we don't have to expose the IntTuple class.

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

Field Details

serialVersionUID

public static final long serialVersionUID

See Also:

• Constant Field Values

Constructor Details

DUSTReadTransformer

public DUSTReadTransformer(int dust_mask,
 int dust_w,
 double dust_t)

Method Details

apply

public GATKRead apply(GATKRead read)

Specified by:

apply in interface Function<GATKRead,GATKRead>

Specified by:

apply in interface SerializableFunction<GATKRead,GATKRead>

sDUST

public static Collection<scala.Tuple2<Integer,Integer>> sDUST(GATKRead read,
 int window,
 double tscore)

Wrapper method for runDUST so that we don't have to expose the IntTuple class.