Interface VariantContextWriter
- All Superinterfaces:
AutoCloseable
,Closeable
- All Known Implementing Classes:
AsyncVariantContextWriter
,SortingVariantContextWriter
this class writes VCF files
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Method Summary
Modifier and TypeMethodDescriptionvoid
add
(VariantContext vc) boolean
void
close()
attempt to close the VCF filevoid
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 Details
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writeHeader
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
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setHeader
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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