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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Constructor Summary
Constructors Constructor Description CompressionHeader()
Create a CompressionHeader using the defaultCRAMEncodingStrategy
CompressionHeader(CRAMVersion cramVersion, InputStream blockStream)
Read a COMPRESSION_HEADER Block from an InputStream and return its contents as a CompressionHeader.CompressionHeader(CompressionHeaderEncodingMap encodingMap)
Create a compression header using the givenCompressionHeaderEncodingMap
.CompressionHeader(CompressionHeaderEncodingMap encodingMap, boolean isAPDelta, boolean isPreserveReadNames, boolean isReferenceRequired)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addTagEncoding(int tagId, ExternalCompressor compressor, EncodingDescriptor params)
CompressionHeaderEncodingMap
getEncodingMap()
Get theCompressionHeaderEncodingMap
for this compression header.SubstitutionMatrix
getSubstitutionMatrix()
Map<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, 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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Constructor Detail
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CompressionHeader
public CompressionHeader()
Create a CompressionHeader using the defaultCRAMEncodingStrategy
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CompressionHeader
public CompressionHeader(CompressionHeaderEncodingMap encodingMap, boolean isAPDelta, boolean isPreserveReadNames, boolean isReferenceRequired)
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CompressionHeader
public CompressionHeader(CompressionHeaderEncodingMap encodingMap)
Create a compression header using the givenCompressionHeaderEncodingMap
.- Parameters:
encodingMap
- the encoding map to use for this compression header
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CompressionHeader
public CompressionHeader(CRAMVersion cramVersion, InputStream blockStream)
Read a COMPRESSION_HEADER Block from an InputStream and return its contents as a CompressionHeader.- Parameters:
cramVersion
- the CRAM versionblockStream
- the stream to read from
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Method Detail
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getEncodingMap
public CompressionHeaderEncodingMap getEncodingMap()
Get theCompressionHeaderEncodingMap
for this compression header.- Returns:
CompressionHeaderEncodingMap
for thisCompressionHeader
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write
public void write(CRAMVersion 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 versionblockStream
- the stream to write to
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isAPDelta
public boolean isAPDelta()
Return true if the header has APDelta set. Coordinate sorted input will use APDelta=true, but it is also permitted for other sort orders to use APDelta=true.- Returns:
- the value of the APDelta flag
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isPreserveReadNames
public boolean isPreserveReadNames()
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getTagEncodingMap
public Map<Integer,EncodingDescriptor> getTagEncodingMap()
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getSubstitutionMatrix
public SubstitutionMatrix getSubstitutionMatrix()
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getTagIDDictionary
public byte[][][] getTagIDDictionary()
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setTagIdDictionary
public void setTagIdDictionary(byte[][][] dictionary)
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setSubstitutionMatrix
public void setSubstitutionMatrix(SubstitutionMatrix substitutionMatrix)
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isReferenceRequired
public boolean isReferenceRequired()
- Returns:
- true if RR is set on this compression header
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addTagEncoding
public void addTagEncoding(int tagId, ExternalCompressor compressor, EncodingDescriptor params)
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