Package vcf

Class RefTargSlidingWindow

  • All Implemented Interfaces:
    java.io.Closeable, java.lang.AutoCloseable, SlidingWindow
    public class RefTargSlidingWindow
extends java.lang.Object
implements SlidingWindow

    Class RefTargSlidingWindow represents a sliding window of reference and target VCF records.

    Instances of class RefTargSlidingWindow are not thread-safe.

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()
      Releases any I/O resources controlled by this object.
      int cumMarkers()
      Returns the number of distinct markers returned in preceding this.nextWindow() method calls.
      int cumTargMarkers()
      Returns the number of distinct target markers returned in preceding this.nextWindow() method calls.
      GeneticMap genMap()
      Returns the genetic map.
      static RefTargSlidingWindow instance​(Par par)
      Constructs and returns a new RefTargSlidingWindow instance for the specified reference and target data.
      java.util.Optional<Window> nextWindow()
      Returns the next sliding window of VCF records.
      Pedigree ped()
      Returns the target sample pedigree data.
      Samples targSamples()
      Returns the target samples.
      java.lang.String toString()
      Returns a string representation of this.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Method Detail

      • instance

        public static RefTargSlidingWindow instance​(Par par)
        Constructs and returns a new RefTargSlidingWindow instance for the specified reference and target data. An exception will be thrown if the command line parameters are incorrectly specified.
        Parameters:
        par - the command line parameters
        Returns:
        a new RefTargSlidingWindow instance for the specified data
        Throws:
        java.lang.IllegalArgumentException - if a VCF record format error is detected or there is no data remaining after sample and marker filtering
        java.lang.NullPointerException - if par == null

      • ped

        public Pedigree ped()
        Description copied from interface: SlidingWindow
        Returns the target sample pedigree data.
        Specified by:
        ped in interface SlidingWindow
        Returns:
        the target sample pedigree data

      • cumTargMarkers

        public int cumTargMarkers()
        Description copied from interface: SlidingWindow
        Returns the number of distinct target markers returned in preceding this.nextWindow() method calls.
        Specified by:
        cumTargMarkers in interface SlidingWindow
        Returns:
        the number of distinct target markers returned in preceding this.nextWindow() method calls

      • cumMarkers

        public int cumMarkers()
        Description copied from interface: SlidingWindow
        Returns the number of distinct markers returned in preceding this.nextWindow() method calls.
        Specified by:
        cumMarkers in interface SlidingWindow
        Returns:
        the number of distinct markers returned in preceding this.nextWindow() method calls

      • nextWindow

        public java.util.Optional<Window> nextWindow()
        Description copied from interface: SlidingWindow
        Returns the next sliding window of VCF records.
        Specified by:
        nextWindow in interface SlidingWindow
        Returns:
        the next sliding window of VCF records or Optional.empty() if there are no additional windows.

      • close

        public void close()
        Description copied from interface: SlidingWindow
        Releases any I/O resources controlled by this object.
        Specified by:
        close in interface java.lang.AutoCloseable
        Specified by:
        close in interface java.io.Closeable
        Specified by:
        close in interface SlidingWindow

      • toString

        public java.lang.String toString()
        Returns a string representation of this. The exact details of the representation are unspecified and subject to change.
        Overrides:
        toString in class java.lang.Object
        Returns:
        a string representation of this.