Class VariantsEncoderOptions

java.lang.Object
htsjdk.beta.plugin.variants.VariantsEncoderOptions
All Implemented Interfaces:
HtsEncoderOptions

public class VariantsEncoderOptions extends Object implements HtsEncoderOptions
  • Constructor Details

    • VariantsEncoderOptions

      public VariantsEncoderOptions()
  • Method Details

    • getBufferSize

      public int getBufferSize()
      Get the buffer size used when writing to an IOPathResource. Defaults to Defaults.NON_ZERO_BUFFER_SIZE.
      Returns:
      the buffer size used when writing to an IOPath
    • setBuffer

      public VariantsEncoderOptions setBuffer(int bufferSize)
      Set an output buffer size to use when writing to an IOPathResource. Does not affect writing to OutputStreams supplied by the user as a OutputStreamResource. Set to 0 for no buffering. Defaults to Defaults.NON_ZERO_BUFFER_SIZE.
      Parameters:
      bufferSize - the buffer size to use
      Returns:
      updated VariantsEncoderOptions
    • isWriteSitesOnly

      public boolean isWriteSitesOnly()
      Determine if sites-only writing is enabled (suppresses writing of genotypes). Defaults to false.
      Returns:
      true if writeSitesOnly is enabled
    • setWriteSitesOnly

      public VariantsEncoderOptions setWriteSitesOnly(boolean writeSitesOnly)
      Set whether only sites are written, without genotypes suppressed. Defaults to false.
      Parameters:
      writeSitesOnly - true if only sites should be written; or false to include genotypes
    • isAllowFieldsMissingFromHeader

      public boolean isAllowFieldsMissingFromHeader()
      Determine if writing fields that are missing from the header is allowed. Defaults to false.
      Returns:
      true if writing fields that are missing from the header is allowed, otherwise false
    • setAllowFieldsMissingFromHeader

      public VariantsEncoderOptions setAllowFieldsMissingFromHeader(boolean allowFieldsMissingFromHeader)
      Set whether writing fields that are missing from the header is allowed. Defaults to false.
      Parameters:
      allowFieldsMissingFromHeader - true to allow missing fields to be written, otherwise false
    • isAsyncIO

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

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

      public boolean isWriteFullFormatField()
      True if only full format fields should always be written (suppress trimming of trailing missing values). Defaults to false.
      Returns:
      true if only full format fields should always be written
    • setWriteFullFormatField

      public VariantsEncoderOptions setWriteFullFormatField(boolean writeFullFormatField)
      Set whether full format fields should always be written (suppress trimming of trailing missing values). Defaults to false.
      Parameters:
      writeFullFormatField - true if full format fields should always be written