Package org.broadinstitute.hellbender.transformers

Interface ReadTransformer

All Superinterfaces:

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

All Known Implementing Classes:

AdapterTrimTransformer, BaseQualityClipReadTransformer, BaseQualityReadTransformer, BQSRReadTransformer, DRAGENMappingQualityReadTransformer, DUSTReadTransformer, IUPACReadTransformer, MappingQualityReadTransformer, MisencodedBaseQualityReadTransformer, NDNCigarReadTransformer, PalindromeArtifactClipReadTransformer, SimpleRepeatMaskTransformer, StripMateNumberTransformer

Functional Interface:

This is a functional interface and can therefore be used as the assignment target for a lambda expression or method reference.

@FunctionalInterface
public interface ReadTransformer
extends UnaryOperator<GATKRead>, SerializableFunction<GATKRead,GATKRead>

Classes which perform transformations from GATKRead -> GATKRead should implement this interface by overriding SerializableFunction<GATKRead,GATKRead>#apply(GATKRead)

Field Summary

Fields

Modifier and Type	Field	Description
static final long	serialVersionUID

Method Summary

Modifier and Type	Method	Description
default ReadTransformer	andThen(ReadTransformer after)
default ReadTransformer	compose(ReadTransformer before)
static ReadTransformer	identity()

Methods inherited from interface java.util.function.Function

andThen, compose

Methods inherited from interface org.broadinstitute.hellbender.utils.SerializableFunction

apply

Field Details

serialVersionUID

static final long serialVersionUID

See Also:

• Constant Field Values

Method Details

andThen

default ReadTransformer andThen(ReadTransformer after)

compose

default ReadTransformer compose(ReadTransformer before)

identity

static ReadTransformer identity()