htsjdk.samtools.cram.structure

Class CRAMEncodingStrategy

java.lang.Object

htsjdk.samtools.cram.structure.CRAMEncodingStrategy

public class CRAMEncodingStrategy
extends java.lang.Object

Parameters that can be set to control the encoding strategy used when writing CRAM.

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_MINIMUM_SINGLE_REFERENCE_SLICE_THRESHOLD
static int	DEFAULT_READS_PER_SLICE

Constructor Summary

Constructors

Constructor and Description
CRAMEncodingStrategy() Create an encoding strategy that uses all default values.

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o)
CompressionHeaderEncodingMap	getCustomCompressionHeaderEncodingMap()
int	getGZIPCompressionLevel()
int	getMinimumSingleReferenceSliceSize()
int	getReadsPerSlice()
int	getSlicesPerContainer()
int	hashCode()
void	setCustomCompressionHeaderEncodingMap(CompressionHeaderEncodingMap encodingMap) Set the CompressionHeaderEncodingMap to use.
CRAMEncodingStrategy	setGZIPCompressionLevel(int compressionLevel)
CRAMEncodingStrategy	setMinimumSingleReferenceSliceSize(int minimumSingleReferenceSliceSize) The minimum number of reads we need to have seen to emit a single-reference slice.
CRAMEncodingStrategy	setReadsPerSlice(int readsPerSlice) Set number of slices per container.
CRAMEncodingStrategy	setSlicesPerContainer(int slicesPerContainer) Set the number of slices per container.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

DEFAULT_MINIMUM_SINGLE_REFERENCE_SLICE_THRESHOLD

public static final int DEFAULT_MINIMUM_SINGLE_REFERENCE_SLICE_THRESHOLD

See Also:

Constant Field Values

DEFAULT_READS_PER_SLICE

public static final int DEFAULT_READS_PER_SLICE

See Also:

Constant Field Values

Constructor Detail

CRAMEncodingStrategy

public CRAMEncodingStrategy()

Create an encoding strategy that uses all default values.

Method Detail

setReadsPerSlice

public CRAMEncodingStrategy setReadsPerSlice(int readsPerSlice)

Set number of slices per container. In some cases, a container containing fewer slices than the requested value will be produced in order to honor the specification rule that all slices in a container must have the same ReferenceContextType. Note: this value must be >= getMinimumSingleReferenceSliceSize().

Parameters:

readsPerSlice - number of slices written per container

Returns:

updated CRAMEncodingStrategy

setMinimumSingleReferenceSliceSize

public CRAMEncodingStrategy setMinimumSingleReferenceSliceSize(int minimumSingleReferenceSliceSize)

The minimum number of reads we need to have seen to emit a single-reference slice. If we've seen fewer than this number, and we have more reads from a different reference context, we prefer to switch to, and subsequently emit, a multiple reference slice, rather than a small single-reference that contains fewer than this number of records. This number must be < the value for getReadsPerSlice()

Parameters:

minimumSingleReferenceSliceSize -

getMinimumSingleReferenceSliceSize

public int getMinimumSingleReferenceSliceSize()

setGZIPCompressionLevel

public CRAMEncodingStrategy setGZIPCompressionLevel(int compressionLevel)

setSlicesPerContainer

public CRAMEncodingStrategy setSlicesPerContainer(int slicesPerContainer)

Set the number of slices per container. If > 1, multiple slices will be placed in the same container if the slices share the same reference context (container records mapped to the same contig). MULTI-REF slices are always emitted as a single contain to avoid conferring MULTI-REF on the next slice, which might otherwise be single-ref; the spec requires a MULTI_REF container to only contain multi-ref slices).

Parameters:

slicesPerContainer - - requested number of slices per container

Returns:

CRAMEncodingStrategy

setCustomCompressionHeaderEncodingMap

public void setCustomCompressionHeaderEncodingMap(CompressionHeaderEncodingMap encodingMap)

Set the CompressionHeaderEncodingMap to use.

Parameters:

encodingMap - the encoding map to use

getCustomCompressionHeaderEncodingMap

public CompressionHeaderEncodingMap getCustomCompressionHeaderEncodingMap()

getGZIPCompressionLevel

public int getGZIPCompressionLevel()

getReadsPerSlice

public int getReadsPerSlice()

getSlicesPerContainer

public int getSlicesPerContainer()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object