Method Detail

• writeHeader

  void writeHeader​(VCFHeader header)

  Writes the header

  Parameters:

  header - header

  Throws:

  IllegalStateException - if header is already written

• close

  void close()

  attempt to close the VCF file

  Specified by:

  close in interface AutoCloseable

  Specified by:

  close in interface 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:

  IllegalStateException - if header or body is already written