Package htsjdk.samtools.cram.build
Class CompressionHeaderFactory
- java.lang.Object
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- htsjdk.samtools.cram.build.CompressionHeaderFactory
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public class CompressionHeaderFactory extends 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.
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Field Summary
Fields Modifier and Type Field Description static int
ALL_BYTES_USED
static int
BYTE_SPACE_SIZE
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Constructor Summary
Constructors Constructor Description CompressionHeaderFactory()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description CompressionHeader
build(List<CramCompressionRecord> records, SubstitutionMatrix substitutionMatrix, boolean sorted)
Decides on compression methods to use for the given records.
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Field Detail
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BYTE_SPACE_SIZE
public static final int BYTE_SPACE_SIZE
- See Also:
- Constant Field Values
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ALL_BYTES_USED
public static final int ALL_BYTES_USED
- See Also:
- Constant Field Values
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Method Detail
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build
public CompressionHeader build(List<CramCompressionRecord> records, SubstitutionMatrix substitutionMatrix, boolean sorted)
Decides on compression methods to use for the given records.- Parameters:
records
- the data to be compressedsubstitutionMatrix
- a matrix of base substitution frequencies, can be null, in which case it is re-calculated.sorted
- if true the records are assumed to be sorted by alignment position- Returns:
CompressionHeader
object describing the encoding chosen for the data
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