Class Writer
- java.lang.Object
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- htsjdk.samtools.cram.encoding.writer.Writer
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public class Writer extends Object
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Field Summary
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Constructor Summary
Constructors Constructor Description Writer()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
isCaptureReadNames()
void
setCaptureReadNames(boolean captureReadNames)
void
write(CramCompressionRecord r)
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Field Detail
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bitFlagsC
public DataWriter<Integer> bitFlagsC
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compBitFlagsC
public DataWriter<Byte> compBitFlagsC
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readLengthC
public DataWriter<Integer> readLengthC
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alStartC
public DataWriter<Integer> alStartC
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readGroupC
public DataWriter<Integer> readGroupC
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readNameC
public DataWriter<byte[]> readNameC
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distanceC
public DataWriter<Integer> distanceC
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tagValueCodecs
public Map<Integer,DataWriter<byte[]>> tagValueCodecs
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numberOfReadFeaturesCodec
public DataWriter<Integer> numberOfReadFeaturesCodec
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featurePositionCodec
public DataWriter<Integer> featurePositionCodec
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featuresCodeCodec
public DataWriter<Byte> featuresCodeCodec
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baseCodec
public DataWriter<Byte> baseCodec
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qualityScoreCodec
public DataWriter<Byte> qualityScoreCodec
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qualityScoreArrayCodec
public DataWriter<byte[]> qualityScoreArrayCodec
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baseSubstitutionCodeCodec
public DataWriter<Byte> baseSubstitutionCodeCodec
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insertionCodec
public DataWriter<byte[]> insertionCodec
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softClipCodec
public DataWriter<byte[]> softClipCodec
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hardClipCodec
public DataWriter<Integer> hardClipCodec
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paddingCodec
public DataWriter<Integer> paddingCodec
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deletionLengthCodec
public DataWriter<Integer> deletionLengthCodec
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mappingQualityScoreCodec
public DataWriter<Integer> mappingQualityScoreCodec
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mateBitFlagsCodec
public DataWriter<Byte> mateBitFlagsCodec
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nextFragmentReferenceSequenceIDCodec
public DataWriter<Integer> nextFragmentReferenceSequenceIDCodec
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nextFragmentAlignmentStart
public DataWriter<Integer> nextFragmentAlignmentStart
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templateSize
public DataWriter<Integer> templateSize
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tagIdListCodec
public DataWriter<Integer> tagIdListCodec
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refIdCodec
public DataWriter<Integer> refIdCodec
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refSkipCodec
public DataWriter<Integer> refSkipCodec
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refId
public int refId
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substitutionMatrix
public SubstitutionMatrix substitutionMatrix
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AP_delta
public boolean AP_delta
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detachedCount
public static int detachedCount
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Method Detail
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write
public void write(CramCompressionRecord r) throws IOException
- Throws:
IOException
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isCaptureReadNames
public boolean isCaptureReadNames()
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setCaptureReadNames
public void setCaptureReadNames(boolean captureReadNames)
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