Class CramCompressionRecord


  • public class CramCompressionRecord
    extends Object
    • 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
      • readGroupID

        public int readGroupID
      • flags

        public int flags
      • mateFlags

        public int mateFlags
      • compressionFlags

        public int compressionFlags
      • 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
      • tagIds

        public byte[] tagIds
      • sliceIndex

        public int sliceIndex
    • Constructor Detail

      • CramCompressionRecord

        public CramCompressionRecord()
    • Method Detail

      • getMateFlags

        public byte getMateFlags()
      • getCompressionFlags

        public byte getCompressionFlags()
      • 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)