org.broadinstitute.hellbender.tools.validation

Class CompareMatrix

java.lang.Object

org.broadinstitute.hellbender.tools.validation.CompareMatrix

All Implemented Interfaces:

java.io.Serializable

public final class CompareMatrix
extends java.lang.Object
implements java.io.Serializable

CompareMatrix contains a square matrix of linear dimension QualityUtils.MAX_SAM_QUAL_SCORE. The elements are counts of the number of times bam 1 had a quality score of i and bam 2 had a quality score of j, (stored in mat[i][j]).

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	dimension

Constructor Summary

Constructors

Constructor and Description
CompareMatrix(byte[] binning)

Method Summary

Modifier and Type	Method and Description
void	add(byte[] first, byte[] second)
CompareMatrix	add(CompareMatrix c)
boolean	hasNonDiagonalElements()
void	printOutResults(java.lang.String outputFilename)

Methods inherited from class java.lang.Object

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

Field Detail

dimension

public static final int dimension

See Also:

Constant Field Values

Constructor Detail

CompareMatrix

public CompareMatrix(byte[] binning)

Method Detail

add

public void add(byte[] first,
                byte[] second)

add

public CompareMatrix add(CompareMatrix c)

hasNonDiagonalElements

public boolean hasNonDiagonalElements()

printOutResults

public void printOutResults(java.lang.String outputFilename)