htsjdk.samtools.cram

Class CRAIEntry

java.lang.Object

htsjdk.samtools.cram.CRAIEntry

All Implemented Interfaces:

java.lang.Cloneable, java.lang.Comparable<CRAIEntry>

public class CRAIEntry
extends java.lang.Object
implements java.lang.Comparable<CRAIEntry>, java.lang.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 java.util.Comparator<CRAIEntry>	byEnd
static java.util.Comparator<CRAIEntry>	byStart
static java.util.Comparator<CRAIEntry>	byStartDesc
long	containerStartOffset
int	sequenceId
int	sliceIndex
int	sliceOffset
int	sliceSize

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
CRAIEntry	clone()
int	compareTo(CRAIEntry o)
static java.util.List<CRAIEntry>	fromContainer(Container container)
static boolean	intersect(CRAIEntry e0, CRAIEntry e1)
java.lang.String	toString()
void	writeToStream(java.io.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 java.util.Comparator<CRAIEntry> byEnd

byStart

public static final java.util.Comparator<CRAIEntry> byStart

byStartDesc

public static java.util.Comparator<CRAIEntry> byStartDesc

Constructor Detail

CRAIEntry

public CRAIEntry()

CRAIEntry

public CRAIEntry(java.lang.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(java.io.OutputStream os)

Serialize the entry to a CRAI index stream.

Parameters:

os - stream to write to

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

fromContainer

public static java.util.List<CRAIEntry> fromContainer(Container container)

compareTo

public int compareTo(CRAIEntry o)

Specified by:

compareTo in interface java.lang.Comparable<CRAIEntry>

clone

public CRAIEntry clone()
                throws java.lang.CloneNotSupportedException

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException

intersect

public static boolean intersect(CRAIEntry e0,
                                CRAIEntry e1)