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
static int	DETACHED_FLAG
static int	DUPLICATE_FLAG
static int	FIRST_SEGMENT_FLAG
int	flags
static int	FORCE_PRESERVE_QS_FLAG
static int	HAS_MATE_DOWNSTREAM_FLAG
int	index
static int	LAST_SEGMENT_FLAG
int	mappingQuality
static int	MATE_NEG_STRAND_FLAG
static int	MATE_UNMAPPED_FLAG
int	mateAlignmentStart
int	mateFlags
int	mateSequenceID
static int	MULTIFRAGMENT_FLAG
static int	NEGATIVE_STRAND_FLAG
CramCompressionRecord	next
CramCompressionRecord	previous
static int	PROPER_PAIR_FLAG
byte[]	qualityScores
byte[]	readBases
java.util.List<ReadFeature>	readFeatures
int	readGroupID
int	readLength
java.lang.String	readName
int	recordsToNextFragment
static int	SECONDARY_ALIGNMENT_FLAG
static int	SEGMENT_UNMAPPED_FLAG
int	sequenceId
java.lang.String	sequenceName
int	sliceIndex
byte[]	tagIds
MutableInt	tagIdsIndex
ReadTag[]	tags
int	templateSize
static int	VENDOR_FILTERED_FLAG

Constructor Summary

Constructors

Constructor and Description
CramCompressionRecord()

Method Summary

Methods

Modifier and Type	Method and Description
void	calculateAlignmentBoundaries()
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	isMateUmapped()
boolean	isMultiFragment()
boolean	isNegativeStrand()
boolean	isProperPair()
boolean	isSecondaryAlignment()
boolean	isSegmentUnmapped()
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	setMateUmapped(boolean mateUmapped)
void	setMultiFragment(boolean multiFragment)
void	setNegativeStrand(boolean negativeStrand)
void	setProperPair(boolean properPair)
void	setSecondaryAlignment(boolean secondaryAlignment)
void	setSegmentUnmapped(boolean segmentUnmapped)
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

MULTIFRAGMENT_FLAG

public static final int MULTIFRAGMENT_FLAG

See Also:

Constant Field Values

PROPER_PAIR_FLAG

public static final int PROPER_PAIR_FLAG

See Also:

Constant Field Values

SEGMENT_UNMAPPED_FLAG

public static final int SEGMENT_UNMAPPED_FLAG

See Also:

Constant Field Values

NEGATIVE_STRAND_FLAG

public static final int NEGATIVE_STRAND_FLAG

See Also:

Constant Field Values

FIRST_SEGMENT_FLAG

public static final int FIRST_SEGMENT_FLAG

See Also:

Constant Field Values

LAST_SEGMENT_FLAG

public static final int LAST_SEGMENT_FLAG

See Also:

Constant Field Values

SECONDARY_ALIGNMENT_FLAG

public static final int SECONDARY_ALIGNMENT_FLAG

See Also:

Constant Field Values

VENDOR_FILTERED_FLAG

public static final int VENDOR_FILTERED_FLAG

See Also:

Constant Field Values

DUPLICATE_FLAG

public static final int DUPLICATE_FLAG

See Also:

Constant Field Values

MATE_NEG_STRAND_FLAG

public static final int MATE_NEG_STRAND_FLAG

See Also:

Constant Field Values

MATE_UNMAPPED_FLAG

public static final int MATE_UNMAPPED_FLAG

See Also:

Constant Field Values

FORCE_PRESERVE_QS_FLAG

public static final int FORCE_PRESERVE_QS_FLAG

See Also:

Constant Field Values

DETACHED_FLAG

public static final int DETACHED_FLAG

See Also:

Constant Field Values

HAS_MATE_DOWNSTREAM_FLAG

public static final int HAS_MATE_DOWNSTREAM_FLAG

See Also:

Constant Field Values

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()

calculateAlignmentBoundaries

public void calculateAlignmentBoundaries()

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)

isMateUmapped

public boolean isMateUmapped()

setMateUmapped

public void setMateUmapped(boolean mateUmapped)

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)

getBAMFlags

public static int getBAMFlags(int cramFlags,
              byte cramMateFlags)