Package vcf

Class MarkerMap

  • public class MarkerMap
extends java.lang.Object

    Class MarkerRecombMap represents genetic map positions and inter-marker genetic distances for a sequence of genomic loci.

    Instances of class MarkerRecombMap are immutable.

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      static MarkerMap create​(GeneticMap genMap, double minGenDist, Markers markers)
      Returns a new MarkerMap instance constructed from the specified data.
      static MarkerMap create​(GeneticMap genMap, Markers markers)
      Returns a new MarkerMap instance constructed from the specified data.
      FloatArray genDist()
      Return a FloatArray of size this.markers().nMarkers() whose k-th element is the genetic distance between the k-th target marker and the previous marker, or 0.0 if (k == 0).
      DoubleArray genPos()
      Returns a DoubleArray of size this.markers().nMarkers() whose k-th element is the genetic map position of the k-th marker.
      static double meanSingleBaseGenDist​(GeneticMap genMap, Markers markers)
      Returns the mean genetic distance between two consecutive base positions.
      FloatArray pRecomb​(float recombIntensity)
      Returns a map of marker index to the probability of recombination in the interval between the marker and the preceding marker.
      MarkerMap restrict​(int[] indices)
      Return a marker map restricted to the specified markers
      MarkerMap restrict​(IntArray indices)
      Return a marker map restricted to the specified markers

      • Methods inherited from class java.lang.Object

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

    • Method Detail

      • create

        public static MarkerMap create​(GeneticMap genMap,
                               Markers markers)
        Returns a new MarkerMap instance constructed from the specified data.
        Parameters:
        genMap - the genetic map
        markers - a list of markers
        Returns:
        a returns new MarkerMap instance
        Throws:
        java.lang.IllegalArgumentException - if markers.marker(0).chromIndex() != markers.marker(markers.nMarkers() - 1).chromIndex()
        java.lang.IllegalArgumentException - if the specified genetic map has no map positions for the specified chromosome
        java.lang.NullPointerException - if genMap == null || markers == null

      • create

        public static MarkerMap create​(GeneticMap genMap,
                               double minGenDist,
                               Markers markers)
        Returns a new MarkerMap instance constructed from the specified data.
        Parameters:
        genMap - the genetic map
        minGenDist - the required minimum cM distance between successive markers
        markers - a list of markers
        Returns:
        a returns new MarkerMap instance
        Throws:
        java.lang.IllegalArgumentException - if markers.marker(0).chromIndex() != markers.marker(markers.nMarkers() - 1).chromIndex()
        java.lang.IllegalArgumentException - if Double.isFinite(minDist) == false
        java.lang.IllegalArgumentException - if the specified genetic map has no map positions for the specified chromosome
        java.lang.NullPointerException - if genMap == null || markers == null

      • meanSingleBaseGenDist

        public static double meanSingleBaseGenDist​(GeneticMap genMap,
                                           Markers markers)
        Returns the mean genetic distance between two consecutive base positions.
        Parameters:
        genMap - the genetic map
        markers - a list of markers
        Returns:
        the mean genetic distance between two consecutive base positions
        Throws:
        java.lang.IllegalArgumentException - if markers.marker(0).chromIndex() != markers.marker(markers.nMarkers() - 1).chromIndex()
        java.lang.IllegalArgumentException - if markers.marker(0).pos() == markers.marker(markers.nMarkers() - 1).pos()
        java.lang.IllegalArgumentException - if the specified genetic map has no map positions for the specified chromosome
        java.lang.NullPointerException - if genMap == null || markers == null

      • restrict

        public MarkerMap restrict​(int[] indices)
        Return a marker map restricted to the specified markers
        Parameters:
        indices - a list of distinct marker indices in increasing order
        Returns:
        a marker map restricted to the specified markers
        Throws:
        java.lang.IndexOutOfBoundsException - if there exists j such that (0 <= j && j < indices.length) such that (indices[j] < 0 || indices[j] >= this.nMarkers())
        java.lang.IllegalArgumentException - if there exists j such that (1 <= j && j < indices.length) such that (indices[j] <= indice[j - 1])
        java.lang.NullPointerException - if indices == null

      • restrict

        public MarkerMap restrict​(IntArray indices)
        Return a marker map restricted to the specified markers
        Parameters:
        indices - a list of distinct marker indices in increasing order
        Returns:
        a marker map restricted to the specified markers
        Throws:
        java.lang.IndexOutOfBoundsException - if there exists j such that (0 <= j && j < indices.length) such that (indices.get(j) < 0 || indices.get(j) >= this.nMarkers())
        java.lang.IllegalArgumentException - if there exists j such that (1 <= j && j < indices.length) such that (indices.get(j) <= indice.get(j - 1))
        java.lang.NullPointerException - if indices == null

      • genPos

        public DoubleArray genPos()
        Returns a DoubleArray of size this.markers().nMarkers() whose k-th element is the genetic map position of the k-th marker.
        Returns:
        the array of genetic map positions

      • genDist

        public FloatArray genDist()
        Return a FloatArray of size this.markers().nMarkers() whose k-th element is the genetic distance between the k-th target marker and the previous marker, or 0.0 if (k == 0).
        Returns:
        a FloatArray of size this.nTargMarkers() whose k-th element is the genetic distance between the k-th target marker and the previous marker,

      • pRecomb

        public FloatArray pRecomb​(float recombIntensity)
        Returns a map of marker index to the probability of recombination in the interval between the marker and the preceding marker.
        Parameters:
        recombIntensity - the intensity of the exponential distribution that gives the probability of transitioning to a random HMM state in a specified cM distance
        Returns:
        a map of marker index to the probability of recombination in the interval between the marker and the preceding marker
        Throws:
        java.lang.IllegalArgumentException - if intensity <= 0.0 || Float.isFinite(intensity)==false