CompressionHeader (htsjdk 2.23.0 API)

java.lang.Object
- htsjdk.samtools.cram.structure.CompressionHeader

public class CompressionHeader
extends Object

Constructor Summary

Constructors
Constructor	Description
`CompressionHeader()`	Create a CompressionHeader using the default `CRAMEncodingStrategy`
`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 given `CompressionHeaderEncodingMap`.
`CompressionHeader(CompressionHeaderEncodingMap encodingMap, boolean isAPDelta, boolean isPreserveReadNames, boolean isReferenceRequired)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addTagEncoding(int tagId, ExternalCompressor compressor, EncodingDescriptor params)`
`CompressionHeaderEncodingMap`	`getEncodingMap()`	Get the `CompressionHeaderEncodingMap` 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.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail
- CompressionHeader
```
public CompressionHeader()
```
  Create a CompressionHeader using the default CRAMEncodingStrategy
- CompressionHeader
```
public CompressionHeader(CompressionHeaderEncodingMap encodingMap,
                         boolean isAPDelta,
                         boolean isPreserveReadNames,
                         boolean isReferenceRequired)
```
- CompressionHeader
```
public CompressionHeader(CompressionHeaderEncodingMap encodingMap)
```
  Create a compression header using the given CompressionHeaderEncodingMap.
  
  Parameters:
  
  encodingMap - the encoding map to use for this compression header
- 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 version
  
  blockStream - the stream to read from

Method Detail

getEncodingMap
```
public CompressionHeaderEncodingMap getEncodingMap()
```
Get the CompressionHeaderEncodingMap for this compression header.

Returns:

CompressionHeaderEncodingMap for this CompressionHeader

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 version

blockStream - the stream to write to

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

isPreserveReadNames
```
public boolean isPreserveReadNames()
```

getTagEncodingMap

public Map<Integer,EncodingDescriptor> getTagEncodingMap()

getSubstitutionMatrix

public SubstitutionMatrix getSubstitutionMatrix()

getTagIDDictionary

public byte[][][] getTagIDDictionary()

setTagIdDictionary

public void setTagIdDictionary(byte[][][] dictionary)

setSubstitutionMatrix

public void setSubstitutionMatrix(SubstitutionMatrix substitutionMatrix)

isReferenceRequired
```
public boolean isReferenceRequired()
```
Returns:

true if RR is set on this compression header

addTagEncoding

public void addTagEncoding(int tagId,
                           ExternalCompressor compressor,
                           EncodingDescriptor params)