Package htsjdk.samtools.cram

Class CRAIEntry

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

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 Details

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 Details

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