Package htsjdk.variant.variantcontext.writer

Interface VariantContextWriter

All Superinterfaces:
AutoCloseable, Closeable
All Known Implementing Classes:
AsyncVariantContextWriter, SortingVariantContextWriter
public interface VariantContextWriter extends Closeable
this class writes VCF files

  • Method Summary

    Modifier and Type
    Method
    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 Details

    • 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