Package htsjdk.variant.variantcontext.writer

Class 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 Detail

      • mostUpstreamWritableLoc

        protected Integer mostUpstreamWritableLoc
        Deprecated.

      • BEFORE_MOST_UPSTREAM_LOC

        protected static final int BEFORE_MOST_UPSTREAM_LOC
        Deprecated.
        See Also:
        Constant Field Values

    • Constructor Detail

      • 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 Detail

      • 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

      • 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.