AsyncVariantContextWriter (htsjdk 2.14.3 API)

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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`add(VariantContext vc)`
`boolean`	`checkError()`
`protected 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 Detail
  - 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 Detail
  - 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

Class AsyncVariantContextWriter

Field Summary

Fields inherited from class htsjdk.samtools.util.AbstractAsyncWriter

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.util.AbstractAsyncWriter

Methods inherited from class java.lang.Object

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

Constructor Detail

AsyncVariantContextWriter

AsyncVariantContextWriter

Method Detail

synchronouslyWrite

synchronouslyClose

getThreadNamePrefix

add

writeHeader

checkError

setHeader