public abstract class AbstractReader
extends java.lang.Object
Constructor and Description |
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AbstractReader() |
public boolean captureReadNames
public byte[][][] tagIdDictionary
public DataReader<java.lang.Integer> bitFlagsCodec
public DataReader<java.lang.Byte> compressionBitFlagsCodec
public DataReader<java.lang.Integer> readLengthCodec
public DataReader<java.lang.Integer> alignmentStartCodec
public DataReader<java.lang.Integer> readGroupCodec
public DataReader<byte[]> readNameCodec
public DataReader<java.lang.Integer> distanceToNextFragmentCodec
public IntHashMap<DataReader<byte[]>> tagValueCodecs
public DataReader<java.lang.Integer> numberOfReadFeaturesCodec
public DataReader<java.lang.Integer> readFeaturePositionCodec
public DataReader<java.lang.Byte> readFeatureCodeCodec
public DataReader<java.lang.Byte> baseCodec
public DataReader<java.lang.Byte> qualityScoreCodec
public DataReader<byte[]> qualityScoresCodec
public DataReader<java.lang.Byte> baseSubstitutionCodec
public DataReader<byte[]> insertionCodec
public DataReader<byte[]> softClipCodec
public DataReader<java.lang.Integer> hardClipCodec
public DataReader<java.lang.Integer> paddingCodec
public DataReader<java.lang.Integer> deletionLengthCodec
public DataReader<java.lang.Integer> mappingScoreCodec
public DataReader<java.lang.Byte> mateBitFlagCodec
public DataReader<java.lang.Integer> mateReferenceIdCodec
public DataReader<java.lang.Integer> mateAlignmentStartCodec
public DataReader<java.lang.Integer> insertSizeCodec
public DataReader<java.lang.Integer> tagIdListCodec
public DataReader<java.lang.Integer> refIdCodec
public DataReader<java.lang.Integer> refSkipCodec
public DataReader<byte[]> basesCodec
public DataReader<byte[]> scoresCodec
public int refId
public boolean APDelta