org.broadinstitute.hellbender.utils.recalibration.covariates

Class QualityScoreCovariate

java.lang.Object

org.broadinstitute.hellbender.utils.recalibration.covariates.QualityScoreCovariate

All Implemented Interfaces:

java.io.Serializable, Covariate

public final class QualityScoreCovariate
extends java.lang.Object
implements Covariate

The Reported Quality Score covariate.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
QualityScoreCovariate(RecalibrationArgumentCollection RAC)

Method Summary

Modifier and Type	Method and Description
java.lang.String	formatKey(int key) Converts the internal representation of the key to String format for file output.
int	keyFromValue(java.lang.Object value) Converts an Object key into a long key using only the lowest numberOfBits() bits Only necessary for on-the-fly recalibration when you have the object, but need to store it in memory in long format.
int	maximumKeyValue() Returns the maximum value possible for any key representing this covariate
void	recordValues(GATKRead read, htsjdk.samtools.SAMFileHeader header, ReadCovariates values, boolean recordIndelValues) Calculates covariate values for all positions in the read.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate

parseNameForReport

Constructor Detail

QualityScoreCovariate

public QualityScoreCovariate(RecalibrationArgumentCollection RAC)

Method Detail

recordValues

public void recordValues(GATKRead read,
                         htsjdk.samtools.SAMFileHeader header,
                         ReadCovariates values,
                         boolean recordIndelValues)

Description copied from interface: Covariate

Calculates covariate values for all positions in the read.

Specified by:

recordValues in interface Covariate

Parameters:

read - the read to calculate the covariates on.

header - SAM header for the read

values - the object to record the covariate values for every base in the read.

recordIndelValues - indicates whether values of the covariate are to be recorded for indels

formatKey

public java.lang.String formatKey(int key)

Description copied from interface: Covariate

Converts the internal representation of the key to String format for file output.

Specified by:

formatKey in interface Covariate

Parameters:

key - the long representation of the key

Returns:

a string representation of the key

keyFromValue

public int keyFromValue(java.lang.Object value)

Description copied from interface: Covariate

Converts an Object key into a long key using only the lowest numberOfBits() bits Only necessary for on-the-fly recalibration when you have the object, but need to store it in memory in long format. For counting covariates the getValues method already returns all values in long format.

Specified by:

keyFromValue in interface Covariate

Parameters:

value - the object corresponding to the covariate

Returns:

a long representation of the object

maximumKeyValue

public int maximumKeyValue()

Description copied from interface: Covariate

Returns the maximum value possible for any key representing this covariate

Specified by:

maximumKeyValue in interface Covariate

Returns:

the maximum value possible for any key representing this covariate