Package htsjdk.variant.variantcontext.writer

Class SortingVariantContextWriter

java.lang.Object
htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
All Implemented Interfaces:
VariantContextWriter, Closeable, AutoCloseable
@Deprecated public class SortingVariantContextWriter extends Object
Deprecated.
9/2017, this class is completely untested and unsupported, there is no replacement at this time if you use this class please file an issue on github or it will be removed at some point in the future
this class writes VCF files, allowing records to be passed in unsorted (up to a certain genomic distance away)

  • Field Details

    • mostUpstreamWritableLoc

      protected Integer mostUpstreamWritableLoc
      Deprecated.

    • BEFORE_MOST_UPSTREAM_LOC

      protected static final int BEFORE_MOST_UPSTREAM_LOC
      Deprecated.
      See Also:

  • Constructor Details

    • SortingVariantContextWriter

      public SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance, boolean takeOwnershipOfInner)
      Deprecated.
      create a local-sorting VCF writer, given an inner VCF writer to write to
      Parameters:
      innerWriter - the VCFWriter to write to
      maxCachingStartDistance - the maximum start distance between records that we'll cache
      takeOwnershipOfInner - Should this Writer close innerWriter when it's done with it

    • SortingVariantContextWriter

      public SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance)
      Deprecated.

  • Method Details

    • noteCurrentRecord

      protected void noteCurrentRecord(VariantContext vc)
      Deprecated.

    • checkError

      public boolean checkError()
      Deprecated.
      Returns:
      true if the underlying stream is a java.io.PrintStream and its checkError returned true, used for pipelines

    • writeHeader

      public void writeHeader(VCFHeader header)
      Deprecated.
      Description copied from interface: VariantContextWriter
      Writes the header
      Specified by:
      writeHeader in interface VariantContextWriter
      Parameters:
      header - header

    • close

      public void close()
      Deprecated.
      attempt to close the VCF file; we need to flush the queue first
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Specified by:
      close in interface VariantContextWriter

    • add

      public void add(VariantContext vc)
      Deprecated.
      add a record to the file
      Specified by:
      add in interface VariantContextWriter
      Parameters:
      vc - the Variant Context object

    • setHeader

      public void setHeader(VCFHeader header)
      Deprecated.
      Description copied from interface: VariantContextWriter
      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
      Specified by:
      setHeader in interface VariantContextWriter
      Parameters:
      header - VCF header

    • toString

      public String toString()
      Deprecated.
      Gets a string representation of this object.
      Overrides:
      toString in class Object
      Returns:
      a string representation of this object

    • emitSafeRecords

      protected void emitSafeRecords()
      Deprecated.