SortingVariantContextWriter (htsjdk 2.8.1 API)

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

All Implemented Interfaces:

VariantContextWriter, Closeable, AutoCloseable
```
public class SortingVariantContextWriter
extends 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 Integer mostUpstreamWritableLoc

Fields
Modifier and Type	Field and Description
`protected static int`	`BEFORE_MOST_UPSTREAM_LOC`
`protected 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

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

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

toString

emitSafeRecords