Package org.broadinstitute.hellbender.transformers

Class MappingQualityReadTransformer

java.lang.Object

org.broadinstitute.hellbender.transformers.MappingQualityReadTransformer

All Implemented Interfaces:

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

public class MappingQualityReadTransformer
extends Object
implements ReadTransformer

A read transformer to modify the mapping quality of reads with MQ=255 to reads with MQ=60

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
MappingQualityReadTransformer(int fromQuality, int toQuality)

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

MappingQualityReadTransformer

public MappingQualityReadTransformer(int fromQuality,
 int toQuality)

Method Details

apply

public GATKRead apply(GATKRead read)

Specified by:

apply in interface Function<GATKRead,GATKRead>

Specified by:

apply in interface SerializableFunction<GATKRead,GATKRead>