public class CramCompressionRecord
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static class |
CramCompressionRecord.BAM_FLAGS |
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 and Description |
---|
CramCompressionRecord() |
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() |
public int index
public int alignmentStart
public int alignmentDelta
public int readLength
public int recordsToNextFragment
public byte[] readBases
public byte[] qualityScores
public java.util.List<ReadFeature> readFeatures
public int readGroupID
public int flags
public int mateFlags
public int compressionFlags
public CramCompressionRecord next
public CramCompressionRecord previous
public int mateSequenceID
public int mateAlignmentStart
public int mappingQuality
public java.lang.String sequenceName
public int sequenceId
public java.lang.String readName
public int templateSize
public ReadTag[] tags
public byte[] tagIds
public MutableInt tagIdsIndex
public int sliceIndex
public byte getMateFlags()
public byte getCompressionFlags()
public boolean equals(java.lang.Object obj)
equals
in class java.lang.Object
public java.lang.String toString()
toString
in class java.lang.Object
public int getAlignmentSpan()
public int getAlignmentEnd()
public boolean isMultiFragment()
public void setMultiFragment(boolean multiFragment)
public boolean isSegmentUnmapped()
public void setSegmentUnmapped(boolean segmentUnmapped)
public boolean isFirstSegment()
public void setFirstSegment(boolean firstSegment)
public boolean isLastSegment()
public void setLastSegment(boolean lastSegment)
public boolean isSecondaryAlignment()
public void setSecondaryAlignment(boolean secondaryAlignment)
public boolean isVendorFiltered()
public void setVendorFiltered(boolean vendorFiltered)
public boolean isProperPair()
public void setProperPair(boolean properPair)
public boolean isDuplicate()
public void setDuplicate(boolean duplicate)
public boolean isNegativeStrand()
public void setNegativeStrand(boolean negativeStrand)
public boolean isMateUnmapped()
public void setMateUnmapped(boolean mateUnmapped)
public boolean isMateNegativeStrand()
public void setMateNegativeStrand(boolean mateNegativeStrand)
public boolean isHasMateDownStream()
public void setHasMateDownStream(boolean hasMateDownStream)
public boolean isDetached()
public void setDetached(boolean detached)
public boolean isForcePreserveQualityScores()
public void setForcePreserveQualityScores(boolean forcePreserveQualityScores)
public boolean isUnknownBases()
public void setUnknownBases(boolean unknownBases)
public boolean isSupplementary()
public void setSupplementary(boolean supplementary)
public static int getBAMFlags(int cramFlags, byte cramMateFlags)