Class CRAMEncodingStrategy

Method Details

• getCramVersion

  public CRAMVersion getCramVersion()

  Returns:

  the CRAM version to write

• setCramVersion

  public CRAMEncodingStrategy setCramVersion(CRAMVersion cramVersion)

  Set the CRAM version to write.

  Parameters:

  cramVersion - the CRAM version (e.g., CramVersions.CRAM_v3 or CramVersions.CRAM_v3_1)

  Returns:

  this strategy for chaining

• setReadsPerSlice

  public CRAMEncodingStrategy setReadsPerSlice(int readsPerSlice)

  Set number of reads per slice. 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 reads written per slice

  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 - the minimum slice size

  Returns:

  this strategy for chaining

• getMinimumSingleReferenceSliceSize

  public int getMinimumSingleReferenceSliceSize()

• setBasesPerSlice

  public CRAMEncodingStrategy setBasesPerSlice(long basesPerSlice)

  Set the maximum accumulated bases per slice. When the accumulated bases in a slice reaches this threshold, the slice is flushed even if getReadsPerSlice() has not been reached. This prevents individual slices from growing pathologically large for long-read data (PacBio HiFi, ONT).

  Setting a value of 0 reverts to the default (getReadsPerSlice() * DEFAULT_BASES_PER_READ), matching htslib's rule.

  Parameters:

  basesPerSlice - maximum bases per slice, or 0 to use the default

  Returns:

  this strategy for chaining

• getBasesPerSlice

  public long getBasesPerSlice()

  Returns:

  the bases-per-slice threshold. If no explicit value was set, returns getReadsPerSlice() * DEFAULT_BASES_PER_READ (matching htslib).

• setGZIPCompressionLevel

  public CRAMEncodingStrategy setGZIPCompressionLevel(int compressionLevel)

  Set the GZIP compression level used for data series compressed with GZIP.

  Parameters:

  compressionLevel - GZIP compression level (0-10)

  Returns:

  this strategy for chaining

• 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 container 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:

  this strategy for chaining

• setCompressorMap

  public CRAMEncodingStrategy setCompressorMap(EnumMap<DataSeries, CompressorDescriptor> compressorMap)

  Set the per-DataSeries compressor map. Each entry maps a DataSeries to the CompressorDescriptor that should be used to compress its block.

  Parameters:

  compressorMap - the compressor map (defensively copied)

  Returns:

  this strategy for chaining

• getCompressorMap

  public EnumMap<DataSeries, CompressorDescriptor> getCompressorMap()

  Returns:

  the per-DataSeries compressor map, or null if not set

• setTrialCandidatesMap

  public CRAMEncodingStrategy setTrialCandidatesMap(EnumMap<DataSeries, List<CompressorDescriptor>> trialCandidatesMap)

  Set additional trial compression candidates per DataSeries. For data series with entries in this map, a TrialCompressor will be created that tries the primary compressor plus all listed candidates, selecting the smallest output.

  Parameters:

  trialCandidatesMap - map of data series to additional candidate descriptors

  Returns:

  this strategy for chaining

• getTrialCandidatesMap

  public EnumMap<DataSeries, List<CompressorDescriptor>> getTrialCandidatesMap()

  Returns:

  the trial candidates map, or null if trial compression is not configured

• setCustomCompressionHeaderEncodingMap

  public void setCustomCompressionHeaderEncodingMap(CompressionHeaderEncodingMap encodingMap)

  Set a pre-built CompressionHeaderEncodingMap that bypasses the compressor map. This is an advanced override intended for tests that need low-level control over encoding descriptors. When set, CompressionHeaderFactory will use this map directly instead of building one from the compressor map.

  Parameters:

  encodingMap - the encoding map to use, or null to use the compressor map

• getCustomCompressionHeaderEncodingMap

  public CompressionHeaderEncodingMap getCustomCompressionHeaderEncodingMap()

  Returns:

  the custom encoding map, or null if the compressor map should be used

• setStoreNM

  public CRAMEncodingStrategy setStoreNM(boolean storeNM)

  Set whether to store the NM:i tag verbatim. When false (default), NM is stripped during encoding for mapped reads and regenerated from features + reference during decoding. Matches htslib's CRAM_OPT_STORE_NM option.

  Parameters:

  storeNM - true to store NM verbatim, false to strip and regenerate

  Returns:

  this strategy for chaining

• getStoreNM

  public boolean getStoreNM()

  Returns:

  whether NM:i tags are stored verbatim (false = stripped and regenerated)

• setStoreMD

  public CRAMEncodingStrategy setStoreMD(boolean storeMD)

  Set whether to store the MD:Z tag verbatim. When false (default), MD is stripped during encoding for mapped reads and regenerated from features + reference during decoding. Matches htslib's CRAM_OPT_STORE_MD option.

  Parameters:

  storeMD - true to store MD verbatim, false to strip and regenerate

  Returns:

  this strategy for chaining

• getStoreMD

  public boolean getStoreMD()

  Returns:

  whether MD:Z tags are stored verbatim (false = stripped and regenerated)

• getGZIPCompressionLevel

  public int getGZIPCompressionLevel()

• getReadsPerSlice

  public int getReadsPerSlice()

• getSlicesPerContainer

  public int getSlicesPerContainer()

• toString

  public String toString()

  Overrides:

  toString in class Object

• equals

  public boolean equals(Object o)

  Overrides:

  equals in class Object

• hashCode

  public int hashCode()

  Overrides:

  hashCode in class Object