Package org.broadinstitute.hellbender.transformers

Class BaseQualityClipReadTransformer

java.lang.Object

org.broadinstitute.hellbender.transformers.BaseQualityClipReadTransformer

All Implemented Interfaces:

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

public final class BaseQualityClipReadTransformer
extends Object
implements ReadTransformer

Clips reads on both ends using base quality scores

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
BaseQualityClipReadTransformer(int trim_thresh)

Method Summary

Modifier and Type	Method	Description
GATKRead	apply(GATKRead read)	Clip bases on the right end of the read from
int	getLeftClipPoint(byte[] quals)	Returns left clip point or -1 if no clip
int	getRightClipPoint(byte[] quals)	Returns right clip point or -1 if no clip

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

BaseQualityClipReadTransformer

public BaseQualityClipReadTransformer(int trim_thresh)

Method Details

apply

public GATKRead apply(GATKRead read)

Clip bases on the right end of the read from

argmax_x{ \sum{i = x + 1}^l (qTrimmingThreshold - qual).

Walk through the read from the right end (in machine cycle order) to the left end, calculating the running sum of qTrimmingThreshold - qual. While we do this, we track the maximum value of this sum where the delta > 0. After the loop, clipPoint is either -1 (don't do anything) or the clipping index in the read (from the end). Repeat in reverse to clip the left end of the read.

Specified by:

apply in interface Function<GATKRead,GATKRead>

Specified by:

apply in interface SerializableFunction<GATKRead,GATKRead>

getRightClipPoint

public int getRightClipPoint(byte[] quals)

Returns right clip point or -1 if no clip

getLeftClipPoint

public int getLeftClipPoint(byte[] quals)

Returns left clip point or -1 if no clip