htsjdk.samtools.cram.structure

Class CramCompressionRecord

java.lang.Object

htsjdk.samtools.cram.structure.CramCompressionRecord

public class CramCompressionRecord
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CramCompressionRecord.BAM_FLAGS

Field Summary

Fields

Modifier and Type	Field and Description
int	alignmentDelta
int	alignmentStart
int	compressionFlags
int	flags
int	index
int	mappingQuality
int	mateAlignmentStart
int	mateFlags
int	mateSequenceID
CramCompressionRecord	next
CramCompressionRecord	previous
byte[]	qualityScores
byte[]	readBases
java.util.List<ReadFeature>	readFeatures
int	readGroupID
int	readLength
java.lang.String	readName
int	recordsToNextFragment
int	sequenceId
java.lang.String	sequenceName
int	sliceIndex
byte[]	tagIds
MutableInt	tagIdsIndex
ReadTag[]	tags
int	templateSize

Constructor Summary

Constructors

Constructor and Description
CramCompressionRecord()

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object obj)
int	getAlignmentEnd()
int	getAlignmentSpan()
static int	getBAMFlags(int cramFlags, byte cramMateFlags)
byte	getCompressionFlags()
byte	getMateFlags()
boolean	isDetached()
boolean	isDuplicate()
boolean	isFirstSegment()
boolean	isForcePreserveQualityScores()
boolean	isHasMateDownStream()
boolean	isLastSegment()
boolean	isMateNegativeStrand()
boolean	isMateUnmapped()
boolean	isMultiFragment()
boolean	isNegativeStrand()
boolean	isProperPair()
boolean	isSecondaryAlignment()
boolean	isSegmentUnmapped()
boolean	isSupplementary()
boolean	isUnknownBases()
boolean	isVendorFiltered()
void	setDetached(boolean detached)
void	setDuplicate(boolean duplicate)
void	setFirstSegment(boolean firstSegment)
void	setForcePreserveQualityScores(boolean forcePreserveQualityScores)
void	setHasMateDownStream(boolean hasMateDownStream)
void	setLastSegment(boolean lastSegment)
void	setMateNegativeStrand(boolean mateNegativeStrand)
void	setMateUnmapped(boolean mateUnmapped)
void	setMultiFragment(boolean multiFragment)
void	setNegativeStrand(boolean negativeStrand)
void	setProperPair(boolean properPair)
void	setSecondaryAlignment(boolean secondaryAlignment)
void	setSegmentUnmapped(boolean segmentUnmapped)
void	setSupplementary(boolean supplementary)
void	setUnknownBases(boolean unknownBases)
void	setVendorFiltered(boolean vendorFiltered)
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

index

public int index

alignmentStart

public int alignmentStart

alignmentDelta

public int alignmentDelta

readLength

public int readLength

recordsToNextFragment

public int recordsToNextFragment

readBases

public byte[] readBases

qualityScores

public byte[] qualityScores

readFeatures

public java.util.List<ReadFeature> readFeatures

readGroupID

public int readGroupID

flags

public int flags

mateFlags

public int mateFlags

compressionFlags

public int compressionFlags

next

public CramCompressionRecord next

previous

public CramCompressionRecord previous

mateSequenceID

public int mateSequenceID

mateAlignmentStart

public int mateAlignmentStart

mappingQuality

public int mappingQuality

sequenceName

public java.lang.String sequenceName

sequenceId

public int sequenceId

readName

public java.lang.String readName

templateSize

public int templateSize

tags

public ReadTag[] tags

tagIds

public byte[] tagIds

tagIdsIndex

public MutableInt tagIdsIndex

sliceIndex

public int sliceIndex

Constructor Detail

CramCompressionRecord

public CramCompressionRecord()

Method Detail

getMateFlags

public byte getMateFlags()

getCompressionFlags

public byte getCompressionFlags()

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getAlignmentSpan

public int getAlignmentSpan()

getAlignmentEnd

public int getAlignmentEnd()

isMultiFragment

public boolean isMultiFragment()

setMultiFragment

public void setMultiFragment(boolean multiFragment)

isSegmentUnmapped

public boolean isSegmentUnmapped()

setSegmentUnmapped

public void setSegmentUnmapped(boolean segmentUnmapped)

isFirstSegment

public boolean isFirstSegment()

setFirstSegment

public void setFirstSegment(boolean firstSegment)

isLastSegment

public boolean isLastSegment()

setLastSegment

public void setLastSegment(boolean lastSegment)

isSecondaryAlignment

public boolean isSecondaryAlignment()

setSecondaryAlignment

public void setSecondaryAlignment(boolean secondaryAlignment)

isVendorFiltered

public boolean isVendorFiltered()

setVendorFiltered

public void setVendorFiltered(boolean vendorFiltered)

isProperPair

public boolean isProperPair()

setProperPair

public void setProperPair(boolean properPair)

isDuplicate

public boolean isDuplicate()

setDuplicate

public void setDuplicate(boolean duplicate)

isNegativeStrand

public boolean isNegativeStrand()

setNegativeStrand

public void setNegativeStrand(boolean negativeStrand)

isMateUnmapped

public boolean isMateUnmapped()

setMateUnmapped

public void setMateUnmapped(boolean mateUnmapped)

isMateNegativeStrand

public boolean isMateNegativeStrand()

setMateNegativeStrand

public void setMateNegativeStrand(boolean mateNegativeStrand)

isHasMateDownStream

public boolean isHasMateDownStream()

setHasMateDownStream

public void setHasMateDownStream(boolean hasMateDownStream)

isDetached

public boolean isDetached()

setDetached

public void setDetached(boolean detached)

isForcePreserveQualityScores

public boolean isForcePreserveQualityScores()

setForcePreserveQualityScores

public void setForcePreserveQualityScores(boolean forcePreserveQualityScores)

isUnknownBases

public boolean isUnknownBases()

setUnknownBases

public void setUnknownBases(boolean unknownBases)

isSupplementary

public boolean isSupplementary()

setSupplementary

public void setSupplementary(boolean supplementary)

getBAMFlags

public static int getBAMFlags(int cramFlags,
                              byte cramMateFlags)