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

All Implemented Interfaces:

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

Constructor Summary

Constructors
Constructor	Description
`CRAIEntry(int sequenceId, int alignmentStart, int alignmentSpan, long containerStartByteOffset, int sliceByteOffsetFromCompressionHeaderStart, int sliceByteSize)`
`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	Description
`int`	`compareTo(CRAIEntry other)`	Sort by numerical order of reference sequence ID, except that unmapped-unplaced reads come last For valid reference sequence ID (placed reads): - sort by alignment start - if alignment start is equal, sort by container offset - if alignment start and container offset are equal, sort by slice offset For unmapped-unplaced reads: - ignore (invalid) alignment start value - sort by container offset - if container offset is equal, sort by slice offset
`boolean`	`equals(Object o)`
`int`	`getAlignmentSpan()`
`int`	`getAlignmentStart()`
`long`	`getContainerStartByteOffset()`
`int`	`getSequenceId()`
`int`	`getSliceByteOffsetFromCompressionHeaderStart()`
`int`	`getSliceByteSize()`
`int`	`hashCode()`
`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
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - CRAIEntry
```
public CRAIEntry(int sequenceId,
                 int alignmentStart,
                 int alignmentSpan,
                 long containerStartByteOffset,
                 int sliceByteOffsetFromCompressionHeaderStart,
                 int sliceByteSize)
```
  - CRAIEntry
```
public CRAIEntry(String line)
```
    Create a CRAI Entry from a serialized CRAI index line.
    
    Parameters:
    
    line - string formatted as a CRAI index entry
- 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
  - compareTo
```
public int compareTo(CRAIEntry other)
```
    Sort by numerical order of reference sequence ID, except that unmapped-unplaced reads come last For valid reference sequence ID (placed reads): - sort by alignment start - if alignment start is equal, sort by container offset - if alignment start and container offset are equal, sort by slice offset For unmapped-unplaced reads: - ignore (invalid) alignment start value - sort by container offset - if container offset is equal, sort by slice offset
    
    Specified by:
    
    compareTo in interface Comparable<CRAIEntry>
    
    Parameters:
    
    other - the CRAIEntry to compare against
    
    Returns:
    
    int representing the comparison result, suitable for ordering
  - intersect
```
public static boolean intersect(CRAIEntry e0,
                                CRAIEntry e1)
```
  - getSequenceId
```
public int getSequenceId()
```
  - getAlignmentStart
```
public int getAlignmentStart()
```
  - getAlignmentSpan
```
public int getAlignmentSpan()
```
  - getContainerStartByteOffset
```
public long getContainerStartByteOffset()
```
  - getSliceByteOffsetFromCompressionHeaderStart
```
public int getSliceByteOffsetFromCompressionHeaderStart()
```
  - getSliceByteSize
```
public int getSliceByteSize()
```
  - equals
```
public boolean equals(Object o)
```
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object

Class CRAIEntry

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

CRAIEntry

CRAIEntry

Method Detail

writeToStream

toString

compareTo

intersect

getSequenceId

getAlignmentStart

getAlignmentSpan

getContainerStartByteOffset

getSliceByteOffsetFromCompressionHeaderStart

getSliceByteSize

equals

hashCode