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BCF2Encoder encodeRawInt(int, BCF2Type) - Method in class. BCF2Encoder encodeRawFloat(double) - Method in class. BCF2Encoder encodeRawChar(byte) - Method in class. encodeRawBytes(int, BCF2Type) - Method in class. Writer detachFromIterator() - Method in class. SAMReadGroupRecord detachedCount - Static variable in class .writer. DownsamplingIteratorFactory.Strategy DESCRIPTION_TAG - Static variable in class htsjdk.samtools. ReadTag description - Variable in enum htsjdk.samtools. ReadTag deriveTypeFromValue(String, Object) - Static method in class. VCFConstants deriveTypeFromKeyAndType(String, Object) - Static method in class. Writer DEPTH_KEY - Static variable in class. AbstractReader deletionLengthCodec - Variable in class .writer. VCFConstants deletionLengthCodec - Variable in class .reader. Deletion DELETION_ALLELE_v3 - Static variable in class. Deletion Deletion(int, int) - Constructor for class .readfeatures. Deletion() - Constructor for class .readfeatures. VariantContextWriterĪ read feature representing a deletion of one or more bases similar to CigarOperator.D. FilteringVariantContextIterator close() - Method in interface. TribbleIndexedFeatureReader close() - Method in class. TabixFeatureReader close() - Method in class ibble. TabixReader close() - Method in class ibble. TabixIteratorLineReader close() - Method in class. SynchronousLineReader close() - Method in class. PositionalBufferedStream close() - Method in class.
![samtools threads samtools threads](https://wikis.utexas.edu/download/attachments/268948473/image2020-6-15_8-47-39.png)
LongLineBufferedReader close() - Method in class. LineIteratorImpl close() - Method in interface. AsciiLineReaderIterator close() - Method in class. AsciiLineReader close() - Method in class. FeatureReader close() - Method in class. AbstractAsyncWriterĪdapter method that closes the provided SOURCE. SRAIndex close() - Method in class htsjdk.samtools. SRAFileReader close() - Method in class htsjdk.samtools.
SRAIndexedSequenceFile close() - Method in class htsjdk.samtools. SRAAlignmentIterator close() - Method in class. SeekableStream close() - Method in class. SeekablePathStream close() - Method in class. SeekableMemoryStream close() - Method in class. SeekableHTTPStream close() - Method in class. SeekableFTPStreamHelper close() - Method in class. SeekableFTPStream close() - Method in class. SeekableFileStream close() - Method in class. SeekableBufferedStream close() - Method in class. ByteArraySeekableStream close() - Method in class. SamReader.PrimitiveSamReaderToSamReaderAdapter close() - Method in class. SamReader.PrimitiveSamReader close() - Method in class htsjdk.samtools. SamReader.AssertingIterator close() - Method in interface htsjdk.samtools. close() - Method in class htsjdk.samtools. Must be called or else file will likely be defective. ByteArrayLenEncoding ByteArraySeekableStream - Class in CompressionHeaderFactory ByteArrayLenEncoding - Class in ByteArrayLenEncoding() - Constructor for class. CRAIEntry BYTE_SPACE_SIZE - Static variable in class. CRAIEntry byStartDesc - Static variable in class. EncodingKey byStart - Static variable in class. CRAIEntry byFirstTwoChars(String) - Static method in enum. DataWriterFactory byEnd - Static variable in class. HuffmanCode buildWriter(BitOutputStream, Map, CompressionHeader, int) - Method in class .writer. Container buildTree(int, T) - Static method in class .huffman. DataReaderFactory buildSlicesTime - Variable in class. buildReader(AbstractReader, BitInputStream, Map, CompressionHeader, int) - Method in class .reader. BlockĬreate a new slice header block with the given uncompressed content. Container buildNewCore(byte) - Static method in class. ContainerFactory buildHeaderTime - Variable in class. SubexponentialIntegerEncoding buildContainer(List) - Method in class. NullEncoding buildCodec(Map, Map) - Method in class. HuffmanIntegerEncoding buildCodec(Map, Map) - Method in class. HuffmanByteEncoding buildCodec(Map, Map) - Method in class .dec. GolombRiceIntegerEncoding buildCodec(Map, Map) - Method in class .dec. GolombLongEncoding buildCodec(Map, Map) - Method in class. GolombIntegerEncoding buildCodec(Map, Map) - Method in class. GammaIntegerEncoding buildCodec(Map, Map) - Method in class. ExternalLongEncoding buildCodec(Map, Map) - Method in class. ExternalIntegerEncoding buildCodec(Map, Map) - Method in class. ExternalByteEncoding buildCodec(Map, Map) - Method in class. ExternalByteArrayEncoding buildCodec(Map, Map) - Method in class.
![samtools threads samtools threads](https://www.basepairtech.com/wp-content/uploads/2016/08/diff-mean.png)
Encoding buildCodec(Map, Map) - Method in class. ByteArrayStopEncoding buildCodec(Map, Map) - Method in interface. ByteArrayLenEncoding buildCodec(Map, Map) - Method in class. BetaIntegerEncoding buildCodec(Map, Map) - Method in class. VCFEncoder buildCodec(Map, Map) - Method in class. buildAlleleStrings(VariantContext) - Method in class. Validate and build the VariantContextWriter.