Interface VariantContextWriter
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- All Superinterfaces:
AutoCloseable
,Closeable
- All Known Implementing Classes:
AsyncVariantContextWriter
,SortingVariantContextWriter
public interface VariantContextWriter extends Closeable
this class writes VCF files
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
add(VariantContext vc)
boolean
checkError()
void
close()
attempt to close the VCF filevoid
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 writervoid
writeHeader(VCFHeader header)
Writes the header
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Method Detail
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writeHeader
void writeHeader(VCFHeader header)
Writes the header- Parameters:
header
- header- Throws:
IllegalStateException
- if header is already written
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close
void close()
attempt to close the VCF file- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
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checkError
boolean checkError()
- Returns:
- true if the underlying stream is a java.io.PrintStream and its checkError returned true, used for pipelines
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add
void add(VariantContext vc)
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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:
IllegalStateException
- if header or body is already written
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