htsjdk.samtools.cram.encoding.writer

Class Writer

java.lang.Object

htsjdk.samtools.cram.encoding.writer.Writer

public class Writer
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
DataWriter<java.lang.Integer>	alStartC
boolean	AP_delta
DataWriter<java.lang.Byte>	baseCodec
DataWriter<java.lang.Byte>	baseSubstitutionCodeCodec
DataWriter<java.lang.Integer>	bitFlagsC
DataWriter<java.lang.Byte>	compBitFlagsC
DataWriter<java.lang.Integer>	deletionLengthCodec
static int	detachedCount
DataWriter<java.lang.Integer>	distanceC
DataWriter<java.lang.Integer>	featurePositionCodec
DataWriter<java.lang.Byte>	featuresCodeCodec
DataWriter<java.lang.Integer>	hardClipCodec
DataWriter<byte[]>	insertionCodec
DataWriter<java.lang.Integer>	mappingQualityScoreCodec
DataWriter<java.lang.Byte>	mateBitFlagsCodec
DataWriter<java.lang.Integer>	nextFragmentAlignmentStart
DataWriter<java.lang.Integer>	nextFragmentReferenceSequenceIDCodec
DataWriter<java.lang.Integer>	numberOfReadFeaturesCodec
DataWriter<java.lang.Integer>	paddingCodec
DataWriter<byte[]>	qualityScoreArrayCodec
DataWriter<java.lang.Byte>	qualityScoreCodec
DataWriter<java.lang.Integer>	readGroupC
DataWriter<java.lang.Integer>	readLengthC
DataWriter<byte[]>	readNameC
int	refId
DataWriter<java.lang.Integer>	refIdCodec
DataWriter<java.lang.Integer>	refSkipCodec
DataWriter<byte[]>	softClipCodec
SubstitutionMatrix	substitutionMatrix
DataWriter<java.lang.Integer>	tagIdListCodec
java.util.Map<java.lang.Integer,DataWriter<byte[]>>	tagValueCodecs
DataWriter<java.lang.Integer>	templateSize

Constructor Summary

Constructors

Constructor and Description
Writer()

Method Summary

Modifier and Type	Method and Description
boolean	isCaptureReadNames()
void	setCaptureReadNames(boolean captureReadNames)
void	write(CramCompressionRecord r)

Methods inherited from class java.lang.Object

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

Field Detail

bitFlagsC

public DataWriter<java.lang.Integer> bitFlagsC

compBitFlagsC

public DataWriter<java.lang.Byte> compBitFlagsC

readLengthC

public DataWriter<java.lang.Integer> readLengthC

alStartC

public DataWriter<java.lang.Integer> alStartC

readGroupC

public DataWriter<java.lang.Integer> readGroupC

readNameC

public DataWriter<byte[]> readNameC

distanceC

public DataWriter<java.lang.Integer> distanceC

tagValueCodecs

public java.util.Map<java.lang.Integer,DataWriter<byte[]>> tagValueCodecs

numberOfReadFeaturesCodec

public DataWriter<java.lang.Integer> numberOfReadFeaturesCodec

featurePositionCodec

public DataWriter<java.lang.Integer> featurePositionCodec

featuresCodeCodec

public DataWriter<java.lang.Byte> featuresCodeCodec

baseCodec

public DataWriter<java.lang.Byte> baseCodec

qualityScoreCodec

public DataWriter<java.lang.Byte> qualityScoreCodec

qualityScoreArrayCodec

public DataWriter<byte[]> qualityScoreArrayCodec

baseSubstitutionCodeCodec

public DataWriter<java.lang.Byte> baseSubstitutionCodeCodec

insertionCodec

public DataWriter<byte[]> insertionCodec

softClipCodec

public DataWriter<byte[]> softClipCodec

hardClipCodec

public DataWriter<java.lang.Integer> hardClipCodec

paddingCodec

public DataWriter<java.lang.Integer> paddingCodec

deletionLengthCodec

public DataWriter<java.lang.Integer> deletionLengthCodec

mappingQualityScoreCodec

public DataWriter<java.lang.Integer> mappingQualityScoreCodec

mateBitFlagsCodec

public DataWriter<java.lang.Byte> mateBitFlagsCodec

nextFragmentReferenceSequenceIDCodec

public DataWriter<java.lang.Integer> nextFragmentReferenceSequenceIDCodec

nextFragmentAlignmentStart

public DataWriter<java.lang.Integer> nextFragmentAlignmentStart

templateSize

public DataWriter<java.lang.Integer> templateSize

tagIdListCodec

public DataWriter<java.lang.Integer> tagIdListCodec

refIdCodec

public DataWriter<java.lang.Integer> refIdCodec

refSkipCodec

public DataWriter<java.lang.Integer> refSkipCodec

refId

public int refId

substitutionMatrix

public SubstitutionMatrix substitutionMatrix

AP_delta

public boolean AP_delta

detachedCount

public static int detachedCount

Constructor Detail

Writer

public Writer()

Method Detail

write

public void write(CramCompressionRecord r)
           throws java.io.IOException

Throws:

java.io.IOException

isCaptureReadNames

public boolean isCaptureReadNames()

setCaptureReadNames

public void setCaptureReadNames(boolean captureReadNames)