CRAIEntry (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.cram.CRAIEntry

All Implemented Interfaces:

Cloneable, Comparable<CRAIEntry>
```
public class CRAIEntry
extends Object
implements Comparable<CRAIEntry>, Cloneable
```
A class representing CRAI index entry: file and alignment offsets for each slice. Created by vadim on 10/08/2015.

Field Summary

Fields
Modifier and Type	Field and Description
`int`	`alignmentSpan`
`int`	`alignmentStart`
`static Comparator<CRAIEntry>`	`byEnd`
`static Comparator<CRAIEntry>`	`byStart`
`static Comparator<CRAIEntry>`	`byStartDesc`
`long`	`containerStartOffset`
`int`	`sequenceId`
`int`	`sliceIndex`
`int`	`sliceOffset`
`int`	`sliceSize`

Constructor Summary

Constructors
Constructor and Description

CRAIEntry()

CRAIEntry(String line)
Create a CRAI Entry from a serialized CRAI index line.

Constructors
Constructor and Description
`CRAIEntry()`
`CRAIEntry(String line)` Create a CRAI Entry from a serialized CRAI index line.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`CRAIEntry`	`clone()`
`int`	`compareTo(CRAIEntry o)`
`static List<CRAIEntry>`	`fromContainer(Container container)`
`static boolean`	`intersect(CRAIEntry e0, CRAIEntry e1)`
`String`	`toString()`
`void`	`writeToStream(OutputStream os)` Serialize the entry to a CRAI index stream.

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

Field Detail

sequenceId
```
public int sequenceId
```

alignmentStart
```
public int alignmentStart
```

alignmentSpan
```
public int alignmentSpan
```

containerStartOffset
```
public long containerStartOffset
```

sliceOffset
```
public int sliceOffset
```

sliceSize
```
public int sliceSize
```

sliceIndex
```
public int sliceIndex
```

byEnd

public static Comparator<CRAIEntry> byEnd

byStart

public static final Comparator<CRAIEntry> byStart

byStartDesc

public static Comparator<CRAIEntry> byStartDesc

Constructor Detail
- CRAIEntry
```
public CRAIEntry()
```
- CRAIEntry
```
public CRAIEntry(String line)
          throws CRAIIndex.CRAIIndexException
```
  Create a CRAI Entry from a serialized CRAI index line.
  
  Parameters:
  
  line - string formatted as a CRAI index entry
  
  Throws:
  
  CRAIIndex.CRAIIndexException

Method Detail

writeToStream
```
public void writeToStream(OutputStream os)
```
Serialize the entry to a CRAI index stream.

Parameters:

os - stream to write to

toString
```
public String toString()
```
Overrides:

toString in class Object

fromContainer

public static List<CRAIEntry> fromContainer(Container container)

compareTo
```
public int compareTo(CRAIEntry o)
```
Specified by:

compareTo in interface Comparable<CRAIEntry>

clone

public CRAIEntry clone()
                throws CloneNotSupportedException

Overrides:: clone in class Object
Throws:: CloneNotSupportedException

intersect

public static boolean intersect(CRAIEntry e0,
                                CRAIEntry e1)

Class CRAIEntry

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

sequenceId

alignmentStart

alignmentSpan

containerStartOffset

sliceOffset

sliceSize

sliceIndex

byEnd

byStart

byStartDesc

Constructor Detail

CRAIEntry

CRAIEntry

Method Detail

writeToStream

toString

fromContainer

compareTo

clone

intersect