public class Writer
extends java.lang.Object
Constructor and Description |
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Writer() |
Modifier and Type | Method and Description |
---|---|
boolean |
isCaptureReadNames() |
void |
setCaptureReadNames(boolean captureReadNames) |
void |
write(CramCompressionRecord r) |
public DataWriter<java.lang.Integer> bitFlagsC
public DataWriter<java.lang.Byte> compBitFlagsC
public DataWriter<java.lang.Integer> readLengthC
public DataWriter<java.lang.Integer> alStartC
public DataWriter<java.lang.Integer> readGroupC
public DataWriter<byte[]> readNameC
public DataWriter<java.lang.Integer> distanceC
public java.util.Map<java.lang.Integer,DataWriter<byte[]>> tagValueCodecs
public DataWriter<java.lang.Integer> numberOfReadFeaturesCodec
public DataWriter<java.lang.Integer> featurePositionCodec
public DataWriter<java.lang.Byte> featuresCodeCodec
public DataWriter<java.lang.Byte> baseCodec
public DataWriter<java.lang.Byte> qualityScoreCodec
public DataWriter<byte[]> qualityScoreArrayCodec
public DataWriter<java.lang.Byte> baseSubstitutionCodeCodec
public DataWriter<byte[]> insertionCodec
public DataWriter<byte[]> softClipCodec
public DataWriter<java.lang.Integer> hardClipCodec
public DataWriter<java.lang.Integer> paddingCodec
public DataWriter<java.lang.Integer> deletionLengthCodec
public DataWriter<java.lang.Integer> mappingQualityScoreCodec
public DataWriter<java.lang.Byte> mateBitFlagsCodec
public DataWriter<java.lang.Integer> nextFragmentReferenceSequenceIDCodec
public DataWriter<java.lang.Integer> nextFragmentAlignmentStart
public DataWriter<java.lang.Integer> templateSize
public DataWriter<java.lang.Integer> tagIdListCodec
public DataWriter<java.lang.Integer> refIdCodec
public DataWriter<java.lang.Integer> refSkipCodec
public int refId
public SubstitutionMatrix substitutionMatrix
public boolean AP_delta
public static int detachedCount
public void write(CramCompressionRecord r) throws java.io.IOException
java.io.IOException
public boolean isCaptureReadNames()
public void setCaptureReadNames(boolean captureReadNames)