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