InfiniumEGTFile (picard 2.22.8 API)

java.lang.Object
- picard.arrays.illumina.InfiniumDataFile
- - picard.arrays.illumina.InfiniumEGTFile

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

Field Summary

Fields
Modifier and Type	Field	Description
`float[][]`	`devR`
`float[][]`	`devTheta`
`static String`	`EXTENSION`
`String`	`manifestName`
`float[][]`	`meanR`
`float[][]`	`meanTheta`
`int[][]`	`n`
`int`	`numCodes`
`String[]`	`rsNames`
`Map<String,Integer>`	`rsNameToIndex`
`float[]`	`totalScore`

Fields inherited from class picard.arrays.illumina.InfiniumDataFile
MAX_UNSIGNED_SHORT

Constructor Summary

Constructors
Constructor Description

InfiniumEGTFile(File clusterFile)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type Method Description

void close()
- 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 String EXTENSION
```
See Also:

Constant Field Values

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 String[] rsNames
```

manifestName
```
public String manifestName
```

numCodes
```
public int numCodes
```

rsNameToIndex

public Map<String,Integer> rsNameToIndex

Constructor Detail

InfiniumEGTFile

public InfiniumEGTFile(File clusterFile)
                throws IOException

Throws:: IOException

Method Detail
- close
```
public void close()
           throws IOException
```
  Specified by:
  
  close in interface AutoCloseable
  
  Throws:
  
  IOException