public class CompressionHeader
extends java.lang.Object
Constructor and Description |
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CompressionHeader()
Create a CompressionHeader using the default
CRAMEncodingStrategy |
CompressionHeader(CompressionHeaderEncodingMap encodingMap)
Create a compression header using the given
CompressionHeaderEncodingMap . |
CompressionHeader(CompressionHeaderEncodingMap encodingMap,
boolean isAPDelta,
boolean isPreserveReadNames,
boolean isReferenceRequired) |
CompressionHeader(CRAMVersion cramVersion,
java.io.InputStream blockStream)
Read a COMPRESSION_HEADER Block from an InputStream and return its contents as a CompressionHeader.
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Modifier and Type | Method and Description |
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void |
addTagEncoding(int tagId,
ExternalCompressor compressor,
EncodingDescriptor params) |
CompressionHeaderEncodingMap |
getEncodingMap()
Get the
CompressionHeaderEncodingMap for this compression header. |
SubstitutionMatrix |
getSubstitutionMatrix() |
java.util.Map<java.lang.Integer,EncodingDescriptor> |
getTagEncodingMap() |
byte[][][] |
getTagIDDictionary() |
boolean |
isAPDelta()
Return true if the header has APDelta set.
|
boolean |
isPreserveReadNames() |
boolean |
isReferenceRequired() |
void |
setSubstitutionMatrix(SubstitutionMatrix substitutionMatrix) |
void |
setTagIdDictionary(byte[][][] dictionary) |
void |
write(CRAMVersion cramVersion,
java.io.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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public CompressionHeader()
CRAMEncodingStrategy
public CompressionHeader(CompressionHeaderEncodingMap encodingMap, boolean isAPDelta, boolean isPreserveReadNames, boolean isReferenceRequired)
public CompressionHeader(CompressionHeaderEncodingMap encodingMap)
CompressionHeaderEncodingMap
.encodingMap
- the encoding map to use for this compression headerpublic CompressionHeader(CRAMVersion cramVersion, java.io.InputStream blockStream)
cramVersion
- the CRAM versionblockStream
- the stream to read frompublic CompressionHeaderEncodingMap getEncodingMap()
CompressionHeaderEncodingMap
for this compression header.CompressionHeaderEncodingMap
for this CompressionHeader
public void write(CRAMVersion cramVersion, java.io.OutputStream blockStream)
cramVersion
- the CRAM versionblockStream
- the stream to write topublic boolean isAPDelta()
public boolean isPreserveReadNames()
public java.util.Map<java.lang.Integer,EncodingDescriptor> getTagEncodingMap()
public SubstitutionMatrix getSubstitutionMatrix()
public byte[][][] getTagIDDictionary()
public void setTagIdDictionary(byte[][][] dictionary)
public void setSubstitutionMatrix(SubstitutionMatrix substitutionMatrix)
public boolean isReferenceRequired()
public void addTagEncoding(int tagId, ExternalCompressor compressor, EncodingDescriptor params)