Package | Description |
---|---|
htsjdk.samtools.cram.encoding.reader | |
htsjdk.samtools.cram.encoding.writer |
Modifier and Type | Field and Description |
---|---|
DataReader<java.lang.Integer> |
AbstractReader.alignmentStartCodec |
DataReader<java.lang.Byte> |
AbstractReader.baseCodec |
DataReader<byte[]> |
AbstractReader.basesCodec |
DataReader<java.lang.Byte> |
AbstractReader.baseSubstitutionCodec |
DataReader<java.lang.Integer> |
AbstractReader.bitFlagsCodec |
DataReader<java.lang.Byte> |
AbstractReader.compressionBitFlagsCodec |
DataReader<java.lang.Integer> |
AbstractReader.deletionLengthCodec |
DataReader<java.lang.Integer> |
AbstractReader.distanceToNextFragmentCodec |
DataReader<java.lang.Integer> |
AbstractReader.hardClipCodec |
DataReader<byte[]> |
AbstractReader.insertionCodec |
DataReader<java.lang.Integer> |
AbstractReader.insertSizeCodec |
DataReader<java.lang.Integer> |
AbstractReader.mappingScoreCodec |
DataReader<java.lang.Integer> |
AbstractReader.mateAlignmentStartCodec |
DataReader<java.lang.Byte> |
AbstractReader.mateBitFlagCodec |
DataReader<java.lang.Integer> |
AbstractReader.mateReferenceIdCodec |
DataReader<java.lang.Integer> |
AbstractReader.numberOfReadFeaturesCodec |
DataReader<java.lang.Integer> |
AbstractReader.paddingCodec |
DataReader<java.lang.Byte> |
AbstractReader.qualityScoreCodec |
DataReader<byte[]> |
AbstractReader.qualityScoresCodec |
DataReader<java.lang.Byte> |
AbstractReader.readFeatureCodeCodec |
DataReader<java.lang.Integer> |
AbstractReader.readFeaturePositionCodec |
DataReader<java.lang.Integer> |
AbstractReader.readGroupCodec |
DataReader<java.lang.Integer> |
AbstractReader.readLengthCodec |
DataReader<byte[]> |
AbstractReader.readNameCodec |
DataReader<java.lang.Integer> |
AbstractReader.refIdCodec |
DataReader<java.lang.Integer> |
AbstractReader.refSkipCodec |
DataReader<byte[]> |
AbstractReader.scoresCodec |
DataReader<byte[]> |
AbstractReader.softClipCodec |
DataReader<java.lang.Integer> |
AbstractReader.tagIdListCodec |
Modifier and Type | Field and Description |
---|---|
DataWriter<java.lang.Integer> |
Writer.alStartC |
DataWriter<java.lang.Byte> |
Writer.baseCodec |
DataWriter<java.lang.Byte> |
Writer.baseSubstitutionCodeCodec |
DataWriter<java.lang.Integer> |
Writer.bitFlagsC |
DataWriter<java.lang.Byte> |
Writer.compBitFlagsC |
DataWriter<java.lang.Integer> |
Writer.deletionLengthCodec |
DataWriter<java.lang.Integer> |
Writer.distanceC |
DataWriter<java.lang.Integer> |
Writer.featurePositionCodec |
DataWriter<java.lang.Byte> |
Writer.featuresCodeCodec |
DataWriter<java.lang.Integer> |
Writer.hardClipCodec |
DataWriter<byte[]> |
Writer.insertionCodec |
DataWriter<java.lang.Integer> |
Writer.mappingQualityScoreCodec |
DataWriter<java.lang.Byte> |
Writer.mateBitFlagsCodec |
DataWriter<java.lang.Integer> |
Writer.nextFragmentAlignmentStart |
DataWriter<java.lang.Integer> |
Writer.nextFragmentReferenceSequenceIDCodec |
DataWriter<java.lang.Integer> |
Writer.numberOfReadFeaturesCodec |
DataWriter<java.lang.Integer> |
Writer.paddingCodec |
DataWriter<byte[]> |
Writer.qualityScoreArrayCodec |
DataWriter<java.lang.Byte> |
Writer.qualityScoreCodec |
DataWriter<java.lang.Integer> |
Writer.readGroupC |
DataWriter<java.lang.Integer> |
Writer.readLengthC |
DataWriter<byte[]> |
Writer.readNameC |
DataWriter<java.lang.Integer> |
Writer.refIdCodec |
DataWriter<java.lang.Integer> |
Writer.refSkipCodec |
DataWriter<byte[]> |
Writer.softClipCodec |
DataWriter<java.lang.Integer> |
Writer.tagIdListCodec |
DataWriter<java.lang.Integer> |
Writer.templateSize |