htsjdk.samtools.cram.build

Class CompressionHeaderFactory

java.lang.Object

htsjdk.samtools.cram.build.CompressionHeaderFactory

public class CompressionHeaderFactory
extends java.lang.Object

A class responsible for decisions about which encodings to use for a given set of records. This particular version relies heavily on GZIP and RANS for better compression.

Field Summary

Fields

Modifier and Type	Field and Description
static int	ALL_BYTES_USED
static int	BYTE_SPACE_SIZE

Constructor Summary

Constructors

Constructor and Description
CompressionHeaderFactory()

Method Summary

Modifier and Type	Method and Description
CompressionHeader	build(java.util.List<CramCompressionRecord> records, boolean coordinateSorted) Decides on compression methods to use for the given records.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

BYTE_SPACE_SIZE

public static final int BYTE_SPACE_SIZE

See Also:

Constant Field Values

ALL_BYTES_USED

public static final int ALL_BYTES_USED

See Also:

Constant Field Values

Constructor Detail

CompressionHeaderFactory

public CompressionHeaderFactory()

Method Detail

build

public CompressionHeader build(java.util.List<CramCompressionRecord> records,
                               boolean coordinateSorted)

Decides on compression methods to use for the given records.

Parameters:

records - the data to be compressed

coordinateSorted - if true the records are assumed to be sorted by alignment position

Returns:

CompressionHeader object describing the encoding chosen for the data