Package htsjdk.samtools.cram.structure
Class CompressionHeader
- java.lang.Object
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- htsjdk.samtools.cram.structure.CompressionHeader
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public class CompressionHeader extends Object
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Field Summary
Fields Modifier and Type Field Description boolean
APDelta
byte[][][]
dictionary
Map<DataSeries,EncodingParams>
encodingMap
Map<Integer,ExternalCompressor>
externalCompressors
List<Integer>
externalIds
boolean
readNamesIncluded
SubstitutionMatrix
substitutionMatrix
Map<Integer,EncodingParams>
tMap
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Constructor Summary
Constructors Constructor Description CompressionHeader()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description byte[][]
getTagIds(int id)
static CompressionHeader
read(int cramVersion, InputStream blockStream)
Read a COMPRESSION_HEADER Block from an InputStream and return its contents as a CompressionHeader We do this instead of reading the InputStream directly because the Block content may be compressedvoid
write(Version cramVersion, OutputStream blockStream)
Write this CompressionHeader out to an internal OutputStream, wrap it in a Block, and write that Block out to the passed-in OutputStream.
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Field Detail
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readNamesIncluded
public boolean readNamesIncluded
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APDelta
public boolean APDelta
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encodingMap
public Map<DataSeries,EncodingParams> encodingMap
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tMap
public Map<Integer,EncodingParams> tMap
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externalCompressors
public final Map<Integer,ExternalCompressor> externalCompressors
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substitutionMatrix
public SubstitutionMatrix substitutionMatrix
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dictionary
public byte[][][] dictionary
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Method Detail
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getTagIds
public byte[][] getTagIds(int id)
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write
public void write(Version cramVersion, OutputStream blockStream)
Write this CompressionHeader out to an internal OutputStream, wrap it in a Block, and write that Block out to the passed-in OutputStream.- Parameters:
cramVersion
- the CRAM major version numberblockStream
- the stream to write to
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read
public static CompressionHeader read(int cramVersion, InputStream blockStream)
Read a COMPRESSION_HEADER Block from an InputStream and return its contents as a CompressionHeader We do this instead of reading the InputStream directly because the Block content may be compressed- Parameters:
cramVersion
- the CRAM versionblockStream
- the stream to read from- Returns:
- a new CompressionHeader from the input
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