Package org.seqdoop.hadoop_bam.util

Class Summary

Class	Description
BGZFBlockIndex	An index into BGZF-compressed files, for BGZFSplitFileInputFormat.
BGZFBlockIndexer	An indexing tool for BGZF-compressed files, making them palatable to BGZFSplitFileInputFormat.
BGZFCodec	A Hadoop CompressionCodec for the BGZF compression format, which reads and writes files with a .bgz suffix.
BGZFEnhancedGzipCodec	A Hadoop CompressionCodec for the BGZF compression format, which reads and writes files with a .gz suffix.
BGZFSplitFileInputFormat<K,V>	An InputFormat for BGZF-compressed files.
BGZFSplitGuesser
ConfHelper
DataInputWrapper
DataOutputWrapper
GetSortedBAMHeader
MurmurHash3	This class implements a hash function giving the first 64 bits of the MurmurHash3_x64_128 hash.
NIOFileUtil
Pair<A,B>	Deprecated This class will be removed in the next major version release (8.0).
SAMFileMerger	Merges headerless BAM or CRAM files produced by KeyIgnoringAnySAMOutputFormat into a single file.
SAMHeaderReader
SAMOutputPreparer
SeekableArrayStream	Deprecated Use ByteArraySeekableStream.
Timer	Deprecated This class will be removed in the next major version release (8.0).
VCFFileMerger	Merges headerless VCF files produced by KeyIgnoringVCFOutputFormat into a single file.
VCFHeaderReader	Can read a VCF header without being told beforehand whether the input is VCF or BCF.
WrapSeekable<S extends InputStream & org.apache.hadoop.fs.Seekable>	Wraps Hadoop's "seekable stream" abstraction so that we can give such a one to BlockCompressedInputStream and retain seekability.