picard.arrays.illumina

Class InfiniumEGTFile

java.lang.Object

picard.arrays.illumina.InfiniumDataFile

picard.arrays.illumina.InfiniumEGTFile

All Implemented Interfaces:

java.lang.AutoCloseable

public class InfiniumEGTFile
extends InfiniumDataFile
implements java.lang.AutoCloseable

A class to parse the contents of an Illumina Infinium cluster (EGT) file A cluster file contains information about the clustering information used in mapping red / green intensity information to genotype calls

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	callVersion
java.lang.String	clusterVersion
java.lang.String	dateCreated
float[][]	devR
float[][]	devTheta
static java.lang.String	EXTENSION
java.lang.String	gencallVersion
boolean	isWGT
java.lang.String	manifestName
float[][]	meanR
float[][]	meanTheta
int[][]	n
java.lang.String	normalizationVersion
int	numCodes
java.lang.String[]	rsNames
java.util.Map<java.lang.String,java.lang.Integer>	rsNameToIndex
float[]	totalScore

Fields inherited from class picard.arrays.illumina.InfiniumDataFile

MAX_UNSIGNED_SHORT

Constructor Summary

Constructors

Constructor and Description
InfiniumEGTFile(java.io.File clusterFile)

Method Summary

Modifier and Type	Method and Description
void	close()
java.lang.String	getManifestName()

Methods inherited from class picard.arrays.illumina.InfiniumDataFile

byteArrayToCharArray, byteArrayToFloat, byteArrayToInt, floatToByteArray, getIdentifier, setIdentifier, shortToByteArray

Methods inherited from class java.lang.Object

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

Field Detail

EXTENSION

public static final java.lang.String EXTENSION

See Also:

Constant Field Values

gencallVersion

public java.lang.String gencallVersion

clusterVersion

public java.lang.String clusterVersion

callVersion

public java.lang.String callVersion

normalizationVersion

public java.lang.String normalizationVersion

dateCreated

public java.lang.String dateCreated

isWGT

public boolean isWGT

n

public int[][] n

meanR

public float[][] meanR

meanTheta

public float[][] meanTheta

devR

public float[][] devR

devTheta

public float[][] devTheta

totalScore

public float[] totalScore

rsNames

public java.lang.String[] rsNames

manifestName

public java.lang.String manifestName

numCodes

public int numCodes

rsNameToIndex

public java.util.Map<java.lang.String,java.lang.Integer> rsNameToIndex

Constructor Detail

InfiniumEGTFile

public InfiniumEGTFile(java.io.File clusterFile)
                throws java.io.IOException

Throws:

java.io.IOException

Method Detail

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.lang.AutoCloseable

Throws:

java.io.IOException

getManifestName

public java.lang.String getManifestName()