Package htsjdk.beta.codecs.reads.bam

Class BAMEncoderOptions

java.lang.Object
htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
public class BAMEncoderOptions extends Object
Encoder options specific to BAM encoders.

  • Field Details

    • DEAFULT_MAX_RECORDS_IN_RAM

      public static final int DEAFULT_MAX_RECORDS_IN_RAM
      See Also:

  • Constructor Details

    • BAMEncoderOptions

      public BAMEncoderOptions()

  • Method Details

    • getOutputBufferSize

      public int getOutputBufferSize()
      Get the output buffer size for these options. This determines the size of the output stream buffer used when writing outputs. Default value is Defaults.BUFFER_SIZE.
      Returns:
      the buffer size for these options

    • setOutputBufferSize

      public BAMEncoderOptions setOutputBufferSize(int outputBufferSize)
      Set the buffer size for these options. This determines the size of the output stream buffer used when writing outputs. Defaults value is Defaults.BUFFER_SIZE.
      Parameters:
      outputBufferSize - the buffer size for these options
      Returns:
      updated options

    • isAsyncIO

      public boolean isAsyncIO()
      Determine if async IO is enabled for these options. Defaults to Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS.
      Returns:
      true if async IO is enabled, otherwise false

    • setAsyncIO

      public BAMEncoderOptions setAsyncIO(boolean asyncIO)
      Set whether to enable async IO for these options.
      Parameters:
      asyncIO - true to enable async IO, false to disable.
      Returns:
      updated options

    • getAsyncOutputBufferSize

      public int getAsyncOutputBufferSize()
      Get the async output buffer size used for these options. If and only if using asynchronous IO sets the maximum number of records that can be buffered per writer before producers will block when trying to write another record. Defaults to AbstractAsyncWriter.DEFAULT_QUEUE_SIZE.
      Returns:
      async output buffer size used for these options

    • setAsyncOutputBufferSize

      public BAMEncoderOptions setAsyncOutputBufferSize(int asyncOutputBufferSize)
      Get the async output buffer size used for these options. If and only if using asynchronous IO, sets the maximum number of records that can be buffered per writer before producers will block when trying to write another record.
      Parameters:
      asyncOutputBufferSize - async output buffer size used for these options
      Returns:
      updated options

    • getTemporaryDirectory

      public IOPath getTemporaryDirectory()
      Get the temporary directory path used for these options. The temporary directory path is used for temporary files created during output sorting operations. Defaults value is IOUtil.getDefaultTmpDirPath().
      Returns:
      the temp directory path to use for these options

    • setTemporaryDirectory

      public BAMEncoderOptions setTemporaryDirectory(IOPath tempDirPath)
      Get the temporary directory path for these options. The temporary directory path is used for temporary files created during output sorting operations. Defaults value is IOUtil.getDefaultTmpDirPath().
      Parameters:
      tempDirPath - temporary directory path to use
      Returns:
      updated options

    • getCompressionLevel

      public int getCompressionLevel()
      Set the compression level for these options. Defaults value is BlockCompressedStreamConstants.DEFAULT_COMPRESSION_LEVEL. See BlockCompressedStreamConstants.DEFAULT_COMPRESSION_LEVEL
      Returns:
      the compression level for these options, 1 <= compressionLevel <= 9

    • setCompressionLevel

      public BAMEncoderOptions setCompressionLevel(int compressionLevel)
      Set the compression level for these options. Defaults value is BlockCompressedStreamConstants.DEFAULT_COMPRESSION_LEVEL.
      Parameters:
      compressionLevel - the compression level for these options, 1 <= compressionLevel <= 9
      Returns:
      updated options

    • getMaxRecordsInRAM

      public int getMaxRecordsInRAM()
      Set the maximum records kept in RAM before spilling to disk for these options. May be null. Default value is Maximum records in RAM determines the amount of memory used by the writer when sorting output during writing. When writing very large sorted SAM files, you may need use this option in order to avoid running out of file handles. The RAM available to the JVM may need to be increased in order to hold the specified number of records in RAM. Defaults value is DEAFULT_MAX_RECORDS_IN_RAM.
      Returns:
      the maximum records kept in ram before spilling to disk for these options

    • setMaxRecordsInRAM

      public BAMEncoderOptions setMaxRecordsInRAM(int maxRecordsInRAM)
      Get the maximum records kept in RAM before spilling to disk for these options. Maximum records in RAM determines the amount of memory used by the writer when sorting output during writing. When writing very large sorted SAM files, you may need use this option in order to avoid running out of file handles. The RAM available to the JVM may need to be increased in order to hold the specified number of records in RAM. Defaults value is DEAFULT_MAX_RECORDS_IN_RAM.
      Parameters:
      maxRecordsInRAM - the maximum records kept in ram before spilling to disk. may be null.
      Returns:
      updated options

    • getDeflaterFactory

      public DeflaterFactory getDeflaterFactory()
      Get the DeflaterFactory for these options. Default value is BlockCompressedOutputStream.getDefaultDeflaterFactory().
      Returns:
      the DeflaterFactory for these options

    • setDeflaterFactory

      public BAMEncoderOptions setDeflaterFactory(DeflaterFactory deflaterFactory)
      Set the DeflaterFactory for these options for these options. Default value is BlockCompressedOutputStream.getDefaultDeflaterFactory().
      Parameters:
      deflaterFactory - the DeflaterFactory for these options
      Returns:
      updated options