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/*
* Copyright (C) 2014-2021 Brian L. Browning
*
* This file is part of Beagle
*
* Beagle is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Beagle is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package vcf;
import blbutil.DoubleArray;
import blbutil.FloatArray;
import ints.IntArray;
/**
* <p>Class {@code MarkerRecombMap} represents genetic map positions and
* inter-marker genetic distances for a sequence of genomic loci.
* </p>
* <p>Instances of class {@code MarkerRecombMap} are immutable.
* </p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public class MarkerMap {
private final DoubleArray genPos;
private final FloatArray genDist;
/**
* Returns a new {@code MarkerMap} instance constructed
* from the specified data.
* @param genMap the genetic map
* @param markers a list of markers
* @return a returns new {@code MarkerMap} instance
* @throws IllegalArgumentException if
* {@code markers.marker(0).chromIndex() != markers.marker(markers.nMarkers() - 1).chromIndex()}
* @throws IllegalArgumentException if the specified genetic map has no
* map positions for the specified chromosome
* @throws NullPointerException if
* {@code genMap == null || markers == null}
*/
public static MarkerMap create(GeneticMap genMap, Markers markers) {
return new MarkerMap(GeneticMap.genPos(genMap, markers));
}
/**
* Returns a new {@code MarkerMap} instance constructed
* from the specified data.
* @param genMap the genetic map
* @param minGenDist the required minimum cM distance between successive
* markers
* @param markers a list of markers
* @return a returns new {@code MarkerMap} instance
* @throws IllegalArgumentException if
* {@code markers.marker(0).chromIndex() != markers.marker(markers.nMarkers() - 1).chromIndex()}
* @throws IllegalArgumentException if {@code Double.isFinite(minDist) == false}
* @throws IllegalArgumentException if the specified genetic map has no
* map positions for the specified chromosome
* @throws NullPointerException if
* {@code genMap == null || markers == null}
*/
public static MarkerMap create(GeneticMap genMap, double minGenDist,
Markers markers) {
return new MarkerMap(GeneticMap.genPos(genMap, minGenDist, markers));
}
/**
* Returns the mean genetic distance between two consecutive base positions.
* @param genMap the genetic map
* @param markers a list of markers
* @return the mean genetic distance between two consecutive base positions
* @throws IllegalArgumentException if
* {@code markers.marker(0).chromIndex() != markers.marker(markers.nMarkers() - 1).chromIndex()}
* @throws IllegalArgumentException if
* {@code markers.marker(0).pos() == markers.marker(markers.nMarkers() - 1).pos()}
* @throws IllegalArgumentException if the specified genetic map has no
* map positions for the specified chromosome
* @throws NullPointerException if {@code genMap == null || markers == null}
*/
public static double meanSingleBaseGenDist(GeneticMap genMap, Markers markers) {
Marker a = markers.marker(0);
Marker b = markers.marker(markers.size()-1);
if (a.chromIndex()!=b.chromIndex()) {
throw new IllegalArgumentException("inconsistent data");
}
if (a.pos()==b.pos()) {
String s = "Window has only one position: CHROM=" + a.chrom() + " POS=" + a.pos();
throw new IllegalArgumentException(s);
}
return Math.abs(genMap.genPos(b)-genMap.genPos(a))
/ Math.abs(b.pos()-a.pos());
}
private MarkerMap(double[] gPos) {
this.genPos = new DoubleArray(gPos);
this.genDist = genDist(gPos);
}
/**
* Return a marker map restricted to the specified markers
* @param indices a list of distinct marker indices in increasing order
* @return a marker map restricted to the specified markers
* @throws IndexOutOfBoundsException if there exists {@code j} such that
* {@code (0 <= j && j < indices.length)} such that
* {@code (indices[j] < 0 || indices[j] >= this.nMarkers())}
* @throws IllegalArgumentException if there exists {@code j} such that
* {@code (1 <= j && j < indices.length)} such that
* {@code (indices[j] <= indice[j - 1])}
* @throws NullPointerException if {@code indices == null}
*/
public MarkerMap restrict(int[] indices) {
double[] gPos = new double[indices.length];
gPos[0] = genPos.get(indices[0]);
for (int j=1; j<indices.length; ++j) {
if (indices[j] <= indices[j-1]) {
throw new IllegalArgumentException(String.valueOf(indices[j]));
}
gPos[j] = genPos.get(indices[j]);
}
return new MarkerMap(gPos);
}
/**
* Return a marker map restricted to the specified markers
* @param indices a list of distinct marker indices in increasing order
* @return a marker map restricted to the specified markers
* @throws IndexOutOfBoundsException if there exists {@code j} such that
* {@code (0 <= j && j < indices.length)} such that
* {@code (indices.get(j) < 0 || indices.get(j) >= this.nMarkers())}
* @throws IllegalArgumentException if there exists {@code j} such that
* {@code (1 <= j && j < indices.length)} such that
* {@code (indices.get(j) <= indice.get(j - 1))}
* @throws NullPointerException if {@code indices == null}
*/
public MarkerMap restrict(IntArray indices) {
double[] gPos = new double[indices.size()];
gPos[0] = genPos.get(indices.get(0));
for (int j=1, n=indices.size(); j<n; ++j) {
if (indices.get(j) <= indices.get(j-1)) {
throw new IllegalArgumentException(String.valueOf(indices.get(j)));
}
gPos[j] = genPos.get(indices.get(j));
}
return new MarkerMap(gPos);
}
private static FloatArray genDist(double[] genPos) {
float minCmDist = 1e-7f;
float[] da = new float[genPos.length];
for (int j=1; j<da.length; ++j) {
da[j] = (float) (genPos[j] - genPos[j-1]);
if (da[j] < minCmDist) {
da[j] = minCmDist;
}
}
return new FloatArray(da);
}
/**
* Returns a {@code DoubleArray} of size {@code this.markers().nMarkers()}
* whose {@code k}-th element is the genetic map position of the
* {@code k}-th marker.
* @return the array of genetic map positions
*/
public DoubleArray genPos() {
return genPos;
}
/**
* Return a {@code FloatArray} of size {@code this.markers().nMarkers()}
* whose {@code k}-th element is the genetic distance between the
* {@code k}-th target marker and the previous marker, or {@code 0.0}
* if {@code (k == 0)}.
* @return a {@code FloatArray} of size {@code this.nTargMarkers()}
* whose {@code k}-th element is the genetic distance between the
* {@code k}-th target marker and the previous marker,
*/
public FloatArray genDist() {
return genDist;
}
/**
* Returns a map of marker index to the probability of recombination
* in the interval between the marker and the preceding marker.
* @param recombIntensity the intensity of the exponential distribution
* that gives the probability of transitioning to a random HMM state
* in a specified cM distance
* @return a map of marker index to the probability of recombination
* in the interval between the marker and the preceding marker
* @throws IllegalArgumentException if
* {@code intensity <= 0.0 || Float.isFinite(intensity)==false}
*/
public FloatArray pRecomb(float recombIntensity) {
if (recombIntensity <= 0.0 || Float.isFinite(recombIntensity)==false) {
throw new IllegalArgumentException(String.valueOf(recombIntensity));
}
double c = -recombIntensity;
float[] pRecomb = new float[genDist.size()];
for (int j=1; j<pRecomb.length; ++j) {
pRecomb[j] = (float) -Math.expm1(c*genDist.get(j));
}
return new FloatArray(pRecomb);
}
}
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