Package org.broadinstitute.hellbender.transformers

Class IUPACReadTransformer

java.lang.Object

org.broadinstitute.hellbender.transformers.IUPACReadTransformer

All Implemented Interfaces:

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

public class IUPACReadTransformer
extends Object
implements ReadTransformer

A read transformer to convert IUPAC bases (i.e. non-ATCGs) to Ns Some references (like human hg38) contain IUPAC bases that can be propagated into the reads when decoding cram This transformation is done in-place without copying

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
IUPACReadTransformer()
IUPACReadTransformer(boolean strictMode)

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

IUPACReadTransformer

public IUPACReadTransformer()

IUPACReadTransformer

public IUPACReadTransformer(boolean strictMode)

Method Details

apply

public GATKRead apply(GATKRead read)

Specified by:

apply in interface Function<GATKRead,GATKRead>

Specified by:

apply in interface SerializableFunction<GATKRead,GATKRead>