Package htsjdk.variant.variantcontext.writer

Class AsyncVariantContextWriter

java.lang.Object

htsjdk.samtools.util.AbstractAsyncWriter<VariantContext>

htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter

All Implemented Interfaces:

VariantContextWriter, Closeable, AutoCloseable

public class AsyncVariantContextWriter
extends AbstractAsyncWriter<VariantContext>
implements VariantContextWriter

AsyncVariantContextWriter that can be wrapped around an underlying AsyncVariantContextWriter to provide asynchronous output. Records added are placed into a queue, the queue is then drained into the underlying VariantContextWriter by a thread owned by the instance. Exceptions experienced by the writer thread will be emitted back to the caller in subsequent calls to either add() or close().

Field Summary

Fields inherited from class htsjdk.samtools.util.AbstractAsyncWriter

DEFAULT_QUEUE_SIZE

Constructor Summary

Constructors

Constructor	Description
AsyncVariantContextWriter(VariantContextWriter out)	Creates a new AsyncVariantContextWriter wrapping the provided VariantContextWriter.
AsyncVariantContextWriter(VariantContextWriter out, int queueSize)	Creates an AsyncVariantContextWriter wrapping the provided VariantContextWriter and using the specified queue size for buffer VariantContexts.

Method Summary

Modifier and Type	Method	Description
void	add(VariantContext vc)
boolean	checkError()
protected final String	getThreadNamePrefix()	Returns the prefix to use when naming threads.
void	setHeader(VCFHeader header)	Sets the VCF header so that data blocks can be written without writing the header Exactly one of writeHeader() or setHeader() should be called when using a writer
protected void	synchronouslyClose()
protected void	synchronouslyWrite(VariantContext item)
void	writeHeader(VCFHeader header)	Writes the header

Methods inherited from class htsjdk.samtools.util.AbstractAsyncWriter

close, write

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.variant.variantcontext.writer.VariantContextWriter

close

Constructor Details

AsyncVariantContextWriter

public AsyncVariantContextWriter(VariantContextWriter out)

Creates a new AsyncVariantContextWriter wrapping the provided VariantContextWriter.

AsyncVariantContextWriter

public AsyncVariantContextWriter(VariantContextWriter out,
 int queueSize)

Creates an AsyncVariantContextWriter wrapping the provided VariantContextWriter and using the specified queue size for buffer VariantContexts.

Method Details

synchronouslyWrite

protected void synchronouslyWrite(VariantContext item)

Specified by:

synchronouslyWrite in class AbstractAsyncWriter<VariantContext>

synchronouslyClose

protected void synchronouslyClose()

Specified by:

synchronouslyClose in class AbstractAsyncWriter<VariantContext>

getThreadNamePrefix

protected final String getThreadNamePrefix()

Description copied from class: AbstractAsyncWriter

Returns the prefix to use when naming threads.

Specified by:

getThreadNamePrefix in class AbstractAsyncWriter<VariantContext>

add

public void add(VariantContext vc)

Specified by:

add in interface VariantContextWriter

writeHeader

public void writeHeader(VCFHeader header)

Description copied from interface: VariantContextWriter

Writes the header

Specified by:

writeHeader in interface VariantContextWriter

Parameters:

header - header

checkError

public boolean checkError()

Specified by:

checkError in interface VariantContextWriter

Returns:

true if the underlying stream is a java.io.PrintStream and its checkError returned true, used for pipelines

setHeader

public void setHeader(VCFHeader header)

Description copied from interface: VariantContextWriter

Sets the VCF header so that data blocks can be written without writing the header Exactly one of writeHeader() or setHeader() should be called when using a writer

Specified by:

setHeader in interface VariantContextWriter

Parameters:

header - VCF header