htsjdk.beta.plugin.variants

Class VariantsEncoderOptions

java.lang.Object

htsjdk.beta.plugin.variants.VariantsEncoderOptions

All Implemented Interfaces:

HtsEncoderOptions

public class VariantsEncoderOptions
extends java.lang.Object
implements HtsEncoderOptions

Constructor Summary

Constructors

Constructor and Description
VariantsEncoderOptions()

Method Summary

Modifier and Type	Method and Description
int	getBufferSize() Get the buffer size used when writing to an IOPathResource.
boolean	isAllowFieldsMissingFromHeader() Determine if writing fields that are missing from the header is allowed.
boolean	isAsyncIO() Determine if async IO is enabled for these options.
boolean	isWriteFullFormatField() True if only full format fields should always be written (suppress trimming of trailing missing values).
boolean	isWriteSitesOnly() Determine if sites-only writing is enabled (suppresses writing of genotypes).
VariantsEncoderOptions	setAllowFieldsMissingFromHeader(boolean allowFieldsMissingFromHeader) Set whether writing fields that are missing from the header is allowed.
VariantsEncoderOptions	setAsyncIO(boolean asyncIO) Set whether to enable async IO for these options.
VariantsEncoderOptions	setBuffer(int bufferSize) Set an output buffer size to use when writing to an IOPathResource.
VariantsEncoderOptions	setWriteFullFormatField(boolean writeFullFormatField) Set whether full format fields should always be written (suppress trimming of trailing missing values).
VariantsEncoderOptions	setWriteSitesOnly(boolean writeSitesOnly) Set whether only sites are written, without genotypes suppressed.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

VariantsEncoderOptions

public VariantsEncoderOptions()

Method Detail

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