@Deprecated
public class SortingVariantContextWriter
extends java.lang.Object
| Modifier and Type | Field and Description |
|---|---|
protected static int |
BEFORE_MOST_UPSTREAM_LOC
Deprecated.
|
protected java.lang.Integer |
mostUpstreamWritableLoc
Deprecated.
|
| 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
|
| 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
|
protected java.lang.Integer mostUpstreamWritableLoc
protected static final int BEFORE_MOST_UPSTREAM_LOC
public SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance, boolean takeOwnershipOfInner)
innerWriter - the VCFWriter to write tomaxCachingStartDistance - the maximum start distance between records that we'll cachetakeOwnershipOfInner - Should this Writer close innerWriter when it's done with itpublic SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance)
protected void noteCurrentRecord(VariantContext vc)
public boolean checkError()
public void writeHeader(VCFHeader header)
VariantContextWriterwriteHeader in interface VariantContextWriterheader - headerpublic void close()
close in interface VariantContextWriterclose in interface java.io.Closeableclose in interface java.lang.AutoCloseablepublic void add(VariantContext vc)
add in interface VariantContextWritervc - the Variant Context objectpublic void setHeader(VCFHeader header)
VariantContextWritersetHeader in interface VariantContextWriterheader - VCF headerpublic java.lang.String toString()
toString in class java.lang.Objectprotected void emitSafeRecords()