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