htsjdk.variant.variantcontext.writer

Interface VariantContextWriter

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable

All Known Implementing Classes:

AsyncVariantContextWriter, SortingVariantContextWriter

public interface VariantContextWriter
extends java.io.Closeable

this class writes VCF files

Method Summary

Modifier and Type	Method and Description
void	add(VariantContext vc)
boolean	checkError()
void	close() attempt to close the VCF file
void	setHeader(VCFHeader header) 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
void	writeHeader(VCFHeader header) Writes the header

Method Detail

writeHeader

void writeHeader(VCFHeader header)

Writes the header

Parameters:

header - header

Throws:

java.lang.IllegalStateException - if header is already written

close

void close()

attempt to close the VCF file

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable

checkError

boolean checkError()

Returns:

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

add

void add(VariantContext vc)

setHeader

void setHeader(VCFHeader header)

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

Parameters:

header - VCF header

Throws:

java.lang.IllegalStateException - if header or body is already written