SortingVariantContextWriter (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.variant.variantcontext.writer.SortingVariantContextWriter

All Implemented Interfaces:

VariantContextWriter, Closeable, AutoCloseable
```
@Deprecated
public class SortingVariantContextWriter
extends Object
```
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

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 Description

protected static int BEFORE_MOST_UPSTREAM_LOC
Deprecated.

protected Integer mostUpstreamWritableLoc
Deprecated.

Fields
Modifier and Type	Field	Description
`protected static int`	`BEFORE_MOST_UPSTREAM_LOC`	Deprecated.
`protected Integer`	`mostUpstreamWritableLoc`	Deprecated.

Constructor Summary

Constructors
Constructor	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

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	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
`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 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 AutoCloseable
    
    Specified by:
    
    close in interface Closeable
    
    Specified by:
    
    close in interface VariantContextWriter
  - 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 String toString()
```
    Deprecated.
    
    Gets a string representation of this object.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    
    a string representation of this object
  - emitSafeRecords
```
protected void emitSafeRecords()
```
    Deprecated.

Class SortingVariantContextWriter

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

mostUpstreamWritableLoc

BEFORE_MOST_UPSTREAM_LOC

Constructor Detail

SortingVariantContextWriter

SortingVariantContextWriter

Method Detail

noteCurrentRecord

checkError

writeHeader

close

add

setHeader

toString

emitSafeRecords