Package org.broadinstitute.hellbender.transformers

Class AdapterTrimTransformer

java.lang.Object

org.broadinstitute.hellbender.transformers.AdapterTrimTransformer

All Implemented Interfaces:

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

public final class AdapterTrimTransformer
extends Object
implements ReadTransformer

Trims (hard clips) adapter sequences from read ends. If the adapter sequence ends before the end of the read, trims the remaining bases as well. Trims the closest-matching adapter sequence. In the case of a tie, trims the adapter that occurs earliest in the read.

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
AdapterTrimTransformer(int maxMismatches, int minClipLength, List<String> adapterSequences)

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

AdapterTrimTransformer

public AdapterTrimTransformer(int maxMismatches,
 int minClipLength,
 List<String> adapterSequences)

Method Details

apply

public GATKRead apply(GATKRead read)

Specified by:

apply in interface Function<GATKRead,GATKRead>

Specified by:

apply in interface SerializableFunction<GATKRead,GATKRead>