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 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 String sequenceName

• sequenceId

  public int sequenceId

• readName

  public 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​(Object obj)

  Overrides:

  equals in class Object

• toString

  public String toString()

  Overrides:

  toString in class 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)