htsjdk.variant.variantcontext.writer

Class SortingVariantContextWriter

java.lang.Object

htsjdk.variant.variantcontext.writer.SortingVariantContextWriter

All Implemented Interfaces:

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

Deprecated.

9/2017, this class is completely untested and unsupported, there is no replacement at this time if you use this class please file an issue on github or it will be removed at some point in the future

@Deprecated
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 Deprecated.
protected java.lang.Integer	mostUpstreamWritableLoc Deprecated.

Constructor Summary

Constructors

Constructor and Description
SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance) Deprecated.
SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance, boolean takeOwnershipOfInner) Deprecated. 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) Deprecated. add a record to the file
boolean	checkError() Deprecated.
void	close() Deprecated. attempt to close the VCF file; we need to flush the queue first
protected void	emitSafeRecords() Deprecated.
protected void	noteCurrentRecord(VariantContext vc) Deprecated.
void	setHeader(VCFHeader header) Deprecated. 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
java.lang.String	toString() Deprecated. Gets a string representation of this object.
void	writeHeader(VCFHeader header) Deprecated. Writes the 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

Deprecated.

BEFORE_MOST_UPSTREAM_LOC

protected static final int BEFORE_MOST_UPSTREAM_LOC

Deprecated.

See Also:

Constant Field Values

Constructor Detail

SortingVariantContextWriter

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

Deprecated.

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)

Deprecated.

Method Detail

noteCurrentRecord

protected void noteCurrentRecord(VariantContext vc)

Deprecated.

checkError

public boolean checkError()

Deprecated.

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)

Deprecated.

Description copied from interface: VariantContextWriter

Writes the header

Specified by:

writeHeader in interface VariantContextWriter

Parameters:

header - header

close

public void close()

Deprecated.

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)

Deprecated.

add a record to the file

Specified by:

add in interface VariantContextWriter

Parameters:

vc - the Variant Context object

setHeader

public void setHeader(VCFHeader header)

Deprecated.

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

toString

public java.lang.String toString()

Deprecated.

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()

Deprecated.