htsjdk.samtools.cram.encoding.reader

Class AbstractReader

java.lang.Object

htsjdk.samtools.cram.encoding.reader.AbstractReader

Direct Known Subclasses:

CramRecordReader, RefSeqIdReader

public abstract class AbstractReader
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
DataReader<java.lang.Integer>	alignmentStartCodec
boolean	APDelta
DataReader<java.lang.Byte>	baseCodec
DataReader<byte[]>	basesCodec
DataReader<java.lang.Byte>	baseSubstitutionCodec
DataReader<java.lang.Integer>	bitFlagsCodec
boolean	captureReadNames
DataReader<java.lang.Byte>	compressionBitFlagsCodec
DataReader<java.lang.Integer>	deletionLengthCodec
DataReader<java.lang.Integer>	distanceToNextFragmentCodec
DataReader<java.lang.Integer>	hardClipCodec
DataReader<byte[]>	insertionCodec
DataReader<java.lang.Integer>	insertSizeCodec
DataReader<java.lang.Integer>	mappingScoreCodec
DataReader<java.lang.Integer>	mateAlignmentStartCodec
DataReader<java.lang.Byte>	mateBitFlagCodec
DataReader<java.lang.Integer>	mateReferenceIdCodec
DataReader<java.lang.Integer>	numberOfReadFeaturesCodec
DataReader<java.lang.Integer>	paddingCodec
DataReader<java.lang.Byte>	qualityScoreCodec
DataReader<byte[]>	qualityScoresCodec
DataReader<java.lang.Byte>	readFeatureCodeCodec
DataReader<java.lang.Integer>	readFeaturePositionCodec
DataReader<java.lang.Integer>	readGroupCodec
DataReader<java.lang.Integer>	readLengthCodec
DataReader<byte[]>	readNameCodec
int	refId
DataReader<java.lang.Integer>	refIdCodec
DataReader<java.lang.Integer>	refSkipCodec
DataReader<byte[]>	scoresCodec
DataReader<byte[]>	softClipCodec
byte[][][]	tagIdDictionary
DataReader<java.lang.Integer>	tagIdListCodec
IntHashMap<DataReader<byte[]>>	tagValueCodecs

Constructor Summary

Constructors

Constructor and Description
AbstractReader()

Method Summary

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

captureReadNames

public boolean captureReadNames

tagIdDictionary

public byte[][][] tagIdDictionary

bitFlagsCodec

public DataReader<java.lang.Integer> bitFlagsCodec

compressionBitFlagsCodec

public DataReader<java.lang.Byte> compressionBitFlagsCodec

readLengthCodec

public DataReader<java.lang.Integer> readLengthCodec

alignmentStartCodec

public DataReader<java.lang.Integer> alignmentStartCodec

readGroupCodec

public DataReader<java.lang.Integer> readGroupCodec

readNameCodec

public DataReader<byte[]> readNameCodec

distanceToNextFragmentCodec

public DataReader<java.lang.Integer> distanceToNextFragmentCodec

tagValueCodecs

public IntHashMap<DataReader<byte[]>> tagValueCodecs

numberOfReadFeaturesCodec

public DataReader<java.lang.Integer> numberOfReadFeaturesCodec

readFeaturePositionCodec

public DataReader<java.lang.Integer> readFeaturePositionCodec

readFeatureCodeCodec

public DataReader<java.lang.Byte> readFeatureCodeCodec

baseCodec

public DataReader<java.lang.Byte> baseCodec

qualityScoreCodec

public DataReader<java.lang.Byte> qualityScoreCodec

qualityScoresCodec

public DataReader<byte[]> qualityScoresCodec

baseSubstitutionCodec

public DataReader<java.lang.Byte> baseSubstitutionCodec

insertionCodec

public DataReader<byte[]> insertionCodec

softClipCodec

public DataReader<byte[]> softClipCodec

hardClipCodec

public DataReader<java.lang.Integer> hardClipCodec

paddingCodec

public DataReader<java.lang.Integer> paddingCodec

deletionLengthCodec

public DataReader<java.lang.Integer> deletionLengthCodec

mappingScoreCodec

public DataReader<java.lang.Integer> mappingScoreCodec

mateBitFlagCodec

public DataReader<java.lang.Byte> mateBitFlagCodec

mateReferenceIdCodec

public DataReader<java.lang.Integer> mateReferenceIdCodec

mateAlignmentStartCodec

public DataReader<java.lang.Integer> mateAlignmentStartCodec

insertSizeCodec

public DataReader<java.lang.Integer> insertSizeCodec

tagIdListCodec

public DataReader<java.lang.Integer> tagIdListCodec

refIdCodec

public DataReader<java.lang.Integer> refIdCodec

refSkipCodec

public DataReader<java.lang.Integer> refSkipCodec

basesCodec

public DataReader<byte[]> basesCodec

scoresCodec

public DataReader<byte[]> scoresCodec

refId

public int refId

APDelta

public boolean APDelta

Constructor Detail

AbstractReader

public AbstractReader()