Package org.broadinstitute.hellbender.transformers

Class DRAGENMappingQualityReadTransformer

java.lang.Object

org.broadinstitute.hellbender.transformers.DRAGENMappingQualityReadTransformer

All Implemented Interfaces:

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

public final class DRAGENMappingQualityReadTransformer
extends Object
implements ReadTransformer

Read transformer intended to replicate DRAGEN behavior for handling mapping qualities. This is necessary because the DRAGEN mapper emits mapping qualities between 0-250 which it emits in the XQ tag for reads. This transformer handles unpacking XQ tagged mapping qualities into the read as well mapping those values to a bounded phreds The current behavior maps it naively into the MQ field with no defense against repeat mapping. TODO handle that, make GT deal directly with new annotation

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static String	EXTENDED_MAPPING_QUALITY_READ_TAG

Constructor Summary

Constructors

Constructor	Description
DRAGENMappingQualityReadTransformer()

Method Summary

Modifier and Type	Method	Description
GATKRead	apply(GATKRead read)
static double	mapMappingQualityToPhredLikelihoodScore(int val)

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

Field Details

EXTENDED_MAPPING_QUALITY_READ_TAG

public static String EXTENDED_MAPPING_QUALITY_READ_TAG

Constructor Details

DRAGENMappingQualityReadTransformer

public DRAGENMappingQualityReadTransformer()

Method Details

mapMappingQualityToPhredLikelihoodScore

public static double mapMappingQualityToPhredLikelihoodScore(int val)

Parameters:

val - mapping quality value (ranged 0-250)

Returns:

a score (as is performed by DRAGEN) corresponding to the phred likelihood of mipmapping event given that mapping quality.

apply

public GATKRead apply(GATKRead read)

Specified by:

apply in interface Function<GATKRead,GATKRead>

Specified by:

apply in interface SerializableFunction<GATKRead,GATKRead>