Package htsjdk.samtools.cram
Class CRAIEntry
- java.lang.Object
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- htsjdk.samtools.cram.CRAIEntry
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- 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.
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Field Summary
Fields Modifier and Type Field 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
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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.
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Field Detail
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sequenceId
public int sequenceId
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alignmentStart
public int alignmentStart
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alignmentSpan
public int alignmentSpan
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containerStartOffset
public long containerStartOffset
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sliceOffset
public int sliceOffset
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sliceSize
public int sliceSize
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sliceIndex
public int sliceIndex
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byEnd
public static Comparator<CRAIEntry> byEnd
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byStart
public static final Comparator<CRAIEntry> byStart
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byStartDesc
public static Comparator<CRAIEntry> byStartDesc
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Constructor Detail
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CRAIEntry
public CRAIEntry()
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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
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Method Detail
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writeToStream
public void writeToStream(OutputStream os)
Serialize the entry to a CRAI index stream.- Parameters:
os
- stream to write to
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compareTo
public int compareTo(CRAIEntry o)
- Specified by:
compareTo
in interfaceComparable<CRAIEntry>
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clone
public CRAIEntry clone() throws CloneNotSupportedException
- Overrides:
clone
in classObject
- Throws:
CloneNotSupportedException
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