Package org.broadinstitute.hellbender.transformers

Class NDNCigarReadTransformer

java.lang.Object

org.broadinstitute.hellbender.transformers.NDNCigarReadTransformer

All Implemented Interfaces:

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

public final class NDNCigarReadTransformer
extends Object
implements ReadTransformer

A read transformer that refactors NDN cigar elements to one N element.

This read transformer will refactor cigar strings that contain N-D-N elements to one N element (with total length of the three refactored elements). This is intended primarily for users of RNA-Seq data handling programs such as TopHat2. Currently we consider that the internal N-D-N motif is illegal and we error out when we encounter it. By refactoring the cigar string of those specific reads, users of TopHat and other tools can circumvent this problem without affecting the rest of their dataset.

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
NDNCigarReadTransformer()

Method Summary

Modifier and Type	Method	Description
GATKRead	apply(GATKRead read)
protected static htsjdk.samtools.Cigar	refactorNDNtoN(htsjdk.samtools.Cigar originalCigar)	Refactor cigar strings that contain N-D-N elements to one N element (with total length of the three refactored elements).

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

NDNCigarReadTransformer

public NDNCigarReadTransformer()

Method Details

apply

public GATKRead apply(GATKRead read)

Specified by:

apply in interface Function<GATKRead,GATKRead>

Specified by:

apply in interface SerializableFunction<GATKRead,GATKRead>

refactorNDNtoN

protected static htsjdk.samtools.Cigar refactorNDNtoN(htsjdk.samtools.Cigar originalCigar)

Refactor cigar strings that contain N-D-N elements to one N element (with total length of the three refactored elements).