Package org.broadinstitute.hellbender.transformers

Class MisencodedBaseQualityReadTransformer

java.lang.Object

org.broadinstitute.hellbender.transformers.MisencodedBaseQualityReadTransformer

All Implemented Interfaces:

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

public final class MisencodedBaseQualityReadTransformer
extends Object
implements ReadTransformer

Checks for and errors out (or fixes if requested) when it detects reads with base qualities that are not encoded with phred-scaled quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: if we are asked to fix the scores then we just subtract 31 from every quality score.

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
MisencodedBaseQualityReadTransformer()

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

MisencodedBaseQualityReadTransformer

public MisencodedBaseQualityReadTransformer()

Method Details

apply

public GATKRead apply(GATKRead read)

Specified by:

apply in interface Function<GATKRead,GATKRead>

Specified by:

apply in interface SerializableFunction<GATKRead,GATKRead>