ReadEndsForMarkDuplicates (picard 2.18.2 API)

java.lang.Object
- picard.sam.util.PhysicalLocationInt
- - picard.sam.util.PhysicalLocationShort
  - - picard.sam.markduplicates.util.ReadEnds
    - - picard.sam.markduplicates.util.ReadEndsForMarkDuplicates

All Implemented Interfaces:

Cloneable, PhysicalLocation

Direct Known Subclasses:

ReadEndsForMarkDuplicatesWithBarcodes
```
public class ReadEndsForMarkDuplicates
extends ReadEnds
implements Cloneable
```
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar

- Field Summary
  
  Fields
  Modifier and Type Field Description
  
  int duplicateSetSize
  
  long read1IndexInFile
  
  long read2IndexInFile
  
  short score
  
  protected static int SIZE_OF
  - Fields inherited from interface picard.sam.util.PhysicalLocation
    NO_VALUE
  - Fields inherited from class picard.sam.util.PhysicalLocationInt
    tile, x, y
  - Fields inherited from class picard.sam.markduplicates.util.ReadEnds
    F, FF, FR, isOpticalDuplicate, libraryId, orientation, orientationForOpticalDuplicates, R, read1Coordinate, read1ReferenceIndex, read2Coordinate, read2ReferenceIndex, readGroup, RF, RR
- Constructor Summary
  
  Constructors
  Constructor Description
  
  ReadEndsForMarkDuplicates()
  
  ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates read)
- Method Summary
  
  All Methods Static Methods Instance Methods Concrete Methods
  Modifier and Type Method Description
  
  ReadEndsForMarkDuplicates clone()
  
  static int getSizeOf()
  - Methods inherited from class java.lang.Object
    equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  - Methods inherited from interface picard.sam.util.PhysicalLocation
    hasLocation
  - Methods inherited from class picard.sam.util.PhysicalLocationInt
    getTile, getX, getY, setTile
  - Methods inherited from class picard.sam.util.PhysicalLocationShort
    setX, setY
  - Methods inherited from class picard.sam.markduplicates.util.ReadEnds
    getLibraryId, getOrientationByte, getReadGroup, isPaired, setLibraryId, setReadGroup

Fields
Modifier and Type	Field	Description
`int`	`duplicateSetSize`
`long`	`read1IndexInFile`
`long`	`read2IndexInFile`
`short`	`score`
`protected static int`	`SIZE_OF`

Constructors
Constructor	Description
`ReadEndsForMarkDuplicates()`
`ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates read)`

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`ReadEndsForMarkDuplicates`	`clone()`
`static int`	`getSizeOf()`

Field Detail

SIZE_OF
```
protected static final int SIZE_OF
```
See Also:

Constant Field Values

score
```
public short score
```

read1IndexInFile
```
public long read1IndexInFile
```

read2IndexInFile
```
public long read2IndexInFile
```

duplicateSetSize
```
public int duplicateSetSize
```

Constructor Detail

ReadEndsForMarkDuplicates
```
public ReadEndsForMarkDuplicates()
```

ReadEndsForMarkDuplicates

public ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates read)

Method Detail

getSizeOf
```
public static int getSizeOf()
```

clone

public ReadEndsForMarkDuplicates clone()

Overrides:: clone in class Object

Class ReadEndsForMarkDuplicates

Field Summary

Fields inherited from interface picard.sam.util.PhysicalLocation

Fields inherited from class picard.sam.util.PhysicalLocationInt

Fields inherited from class picard.sam.markduplicates.util.ReadEnds

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface picard.sam.util.PhysicalLocation

Methods inherited from class picard.sam.util.PhysicalLocationInt

Methods inherited from class picard.sam.util.PhysicalLocationShort

Methods inherited from class picard.sam.markduplicates.util.ReadEnds

Field Detail

SIZE_OF

score

read1IndexInFile

read2IndexInFile

duplicateSetSize

Constructor Detail

ReadEndsForMarkDuplicates

ReadEndsForMarkDuplicates

Method Detail

getSizeOf

clone