Package picard.arrays.illumina
Class InfiniumEGTFile
- java.lang.Object
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- picard.arrays.illumina.InfiniumDataFile
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- picard.arrays.illumina.InfiniumEGTFile
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- All Implemented Interfaces:
AutoCloseable
public class InfiniumEGTFile extends InfiniumDataFile implements 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
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Field Summary
Fields Modifier and Type Field Description String
callVersion
String
clusterVersion
String
dateCreated
float[][]
devR
float[][]
devTheta
static String
EXTENSION
String
gencallVersion
boolean
isWGT
String
manifestName
float[][]
meanR
float[][]
meanTheta
int[][]
n
String
normalizationVersion
int
numCodes
String[]
rsNames
Map<String,Integer>
rsNameToIndex
float[]
totalScore
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Fields inherited from class picard.arrays.illumina.InfiniumDataFile
MAX_UNSIGNED_SHORT
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Constructor Summary
Constructors Constructor Description InfiniumEGTFile(File clusterFile)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
String
getManifestName()
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Methods inherited from class picard.arrays.illumina.InfiniumDataFile
byteArrayToCharArray, byteArrayToFloat, byteArrayToInt, floatToByteArray, getIdentifier, setIdentifier, shortToByteArray
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Field Detail
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EXTENSION
public static final String EXTENSION
- See Also:
- Constant Field Values
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gencallVersion
public String gencallVersion
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clusterVersion
public String clusterVersion
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callVersion
public String callVersion
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normalizationVersion
public String normalizationVersion
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dateCreated
public String dateCreated
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isWGT
public boolean isWGT
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n
public int[][] n
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meanR
public float[][] meanR
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meanTheta
public float[][] meanTheta
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devR
public float[][] devR
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devTheta
public float[][] devTheta
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totalScore
public float[] totalScore
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rsNames
public String[] rsNames
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manifestName
public String manifestName
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numCodes
public int numCodes
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Constructor Detail
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InfiniumEGTFile
public InfiniumEGTFile(File clusterFile) throws IOException
- Throws:
IOException
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Method Detail
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close
public void close() throws IOException
- Specified by:
close
in interfaceAutoCloseable
- Throws:
IOException
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getManifestName
public String getManifestName()
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