Class AbstractReader
- java.lang.Object
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- htsjdk.samtools.cram.encoding.reader.AbstractReader
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- Direct Known Subclasses:
CramRecordReader
,RefSeqIdReader
public abstract class AbstractReader extends Object
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Field Summary
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Constructor Summary
Constructors Constructor Description AbstractReader()
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Field Detail
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captureReadNames
public boolean captureReadNames
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tagIdDictionary
public byte[][][] tagIdDictionary
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bitFlagsCodec
public DataReader<Integer> bitFlagsCodec
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compressionBitFlagsCodec
public DataReader<Byte> compressionBitFlagsCodec
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readLengthCodec
public DataReader<Integer> readLengthCodec
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alignmentStartCodec
public DataReader<Integer> alignmentStartCodec
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readGroupCodec
public DataReader<Integer> readGroupCodec
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readNameCodec
public DataReader<byte[]> readNameCodec
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distanceToNextFragmentCodec
public DataReader<Integer> distanceToNextFragmentCodec
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tagValueCodecs
public IntHashMap<DataReader<byte[]>> tagValueCodecs
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numberOfReadFeaturesCodec
public DataReader<Integer> numberOfReadFeaturesCodec
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readFeaturePositionCodec
public DataReader<Integer> readFeaturePositionCodec
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readFeatureCodeCodec
public DataReader<Byte> readFeatureCodeCodec
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baseCodec
public DataReader<Byte> baseCodec
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qualityScoreCodec
public DataReader<Byte> qualityScoreCodec
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qualityScoresCodec
public DataReader<byte[]> qualityScoresCodec
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baseSubstitutionCodec
public DataReader<Byte> baseSubstitutionCodec
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insertionCodec
public DataReader<byte[]> insertionCodec
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softClipCodec
public DataReader<byte[]> softClipCodec
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hardClipCodec
public DataReader<Integer> hardClipCodec
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paddingCodec
public DataReader<Integer> paddingCodec
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deletionLengthCodec
public DataReader<Integer> deletionLengthCodec
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mappingScoreCodec
public DataReader<Integer> mappingScoreCodec
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mateBitFlagCodec
public DataReader<Byte> mateBitFlagCodec
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mateReferenceIdCodec
public DataReader<Integer> mateReferenceIdCodec
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mateAlignmentStartCodec
public DataReader<Integer> mateAlignmentStartCodec
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insertSizeCodec
public DataReader<Integer> insertSizeCodec
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tagIdListCodec
public DataReader<Integer> tagIdListCodec
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refIdCodec
public DataReader<Integer> refIdCodec
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refSkipCodec
public DataReader<Integer> refSkipCodec
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basesCodec
public DataReader<byte[]> basesCodec
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scoresCodec
public DataReader<byte[]> scoresCodec
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refId
public int refId
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APDelta
public boolean APDelta
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