Chunk (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.Chunk

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Chunk>
```
public class Chunk
extends java.lang.Object
implements java.lang.Cloneable, java.io.Serializable, java.lang.Comparable<Chunk>
```
A [start,stop) file pointer pairing into the BAM file, stored as a BAM file index. A chunk is represented as a single 64-bit value where the high-order 48 bits point to the location of the start of a compressed BGZF block within a BGZF file and the low-order 16 bits point to a position within the decompressed data in the BGZF block. See the SAM/BAM spec for more details.

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description

Chunk(long start, long end)

Constructors
Constructor and Description
`Chunk(long start, long end)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Chunk`	`clone()`
`int`	`compareTo(Chunk chunk)`
`boolean`	`equals(java.lang.Object o)`
`long`	`getChunkEnd()`
`long`	`getChunkStart()`
`int`	`hashCode()`
`boolean`	`isAdjacentTo(Chunk other)` Returns whether two chunks overlap.
`static java.util.List<Chunk>`	`optimizeChunkList(java.util.List<Chunk> chunks, long minimumOffset)`
`boolean`	`overlaps(Chunk other)` Returns whether two chunks overlap.
`protected void`	`setChunkEnd(long value)`
`protected void`	`setChunkStart(long value)`
`java.lang.String`	`toString()`

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - Chunk
```
public Chunk(long start,
             long end)
```
- Method Detail
  - clone
```
public Chunk clone()
```
    Overrides:
    
    clone in class java.lang.Object
  - getChunkStart
```
public long getChunkStart()
```
  - setChunkStart
```
protected void setChunkStart(long value)
```
  - getChunkEnd
```
public long getChunkEnd()
```
  - setChunkEnd
```
protected void setChunkEnd(long value)
```
  - compareTo
```
public int compareTo(Chunk chunk)
```
    Specified by:
    
    compareTo in interface java.lang.Comparable<Chunk>
  - equals
```
public boolean equals(java.lang.Object o)
```
    Overrides:
    
    equals in class java.lang.Object
  - overlaps
```
public boolean overlaps(Chunk other)
```
    Returns whether two chunks overlap.
    
    Parameters:
    
    other - Chunk to which this should be compared.
    
    Returns:
    
    True if the chunks overlap. Returns false if the two chunks abut or are disjoint.
  - isAdjacentTo
```
public boolean isAdjacentTo(Chunk other)
```
    Returns whether two chunks overlap.
    
    Parameters:
    
    other - Chunk to which this should be compared.
    
    Returns:
    
    True if the two chunks are adjacent. Returns false if the chunks overlap or are discontinuous.
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class java.lang.Object
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - optimizeChunkList
```
public static java.util.List<Chunk> optimizeChunkList(java.util.List<Chunk> chunks,
                                                      long minimumOffset)
```
    Parameters:
    
    minimumOffset - Discard chunks that end before this file offset.
    
    Returns:
    
    sorted list of chunks in which adjacent chunks are coalesced.

Class Chunk

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Chunk

Method Detail

clone

getChunkStart

setChunkStart

getChunkEnd

setChunkEnd

compareTo

equals

overlaps

isAdjacentTo

hashCode

toString

optimizeChunkList