htsjdk.variant.variantcontext.writer

Class SortingVariantContextWriter

java.lang.Object

htsjdk.variant.variantcontext.writer.SortingVariantContextWriter

All Implemented Interfaces:

VariantContextWriter, java.io.Closeable, java.lang.AutoCloseable

public class SortingVariantContextWriter
extends java.lang.Object

this class writes VCF files, allowing records to be passed in unsorted (up to a certain genomic distance away)

Field Summary

Fields

Modifier and Type	Field and Description
protected static int	BEFORE_MOST_UPSTREAM_LOC
protected java.lang.Integer	mostUpstreamWritableLoc

Constructor Summary

Constructors

Constructor and Description
SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance)
SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance, boolean takeOwnershipOfInner) create a local-sorting VCF writer, given an inner VCF writer to write to

Method Summary

Modifier and Type	Method and Description
void	add(VariantContext vc) add a record to the file
boolean	checkError()
void	close() attempt to close the VCF file; we need to flush the queue first
protected void	emitSafeRecords()
protected void	noteCurrentRecord(VariantContext vc)
java.lang.String	toString() Gets a string representation of this object.
void	writeHeader(VCFHeader header)

Methods inherited from class java.lang.Object

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

Field Detail

mostUpstreamWritableLoc

protected java.lang.Integer mostUpstreamWritableLoc

BEFORE_MOST_UPSTREAM_LOC

protected static final int BEFORE_MOST_UPSTREAM_LOC

See Also:

Constant Field Values

Constructor Detail

SortingVariantContextWriter

public SortingVariantContextWriter(VariantContextWriter innerWriter,
                                   int maxCachingStartDistance,
                                   boolean takeOwnershipOfInner)

create a local-sorting VCF writer, given an inner VCF writer to write to

Parameters:

innerWriter - the VCFWriter to write to

maxCachingStartDistance - the maximum start distance between records that we'll cache

takeOwnershipOfInner - Should this Writer close innerWriter when it's done with it

SortingVariantContextWriter

public SortingVariantContextWriter(VariantContextWriter innerWriter,
                                   int maxCachingStartDistance)

Method Detail

noteCurrentRecord

protected void noteCurrentRecord(VariantContext vc)

checkError

public boolean checkError()

Returns:

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

writeHeader

public void writeHeader(VCFHeader header)

Specified by:

writeHeader in interface VariantContextWriter

close

public void close()

attempt to close the VCF file; we need to flush the queue first

Specified by:

close in interface VariantContextWriter

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

add

public void add(VariantContext vc)

add a record to the file

Specified by:

add in interface VariantContextWriter

Parameters:

vc - the Variant Context object

toString

public java.lang.String toString()

Gets a string representation of this object.

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this object

emitSafeRecords

protected void emitSafeRecords()