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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 phase;
import blbutil.DoubleArray;
import blbutil.FloatArray;
import ints.IntArray;
import ints.IntList;
import ints.WrappedIntArray;
import java.util.stream.IntStream;
import vcf.GT;
import vcf.MarkerMap;
/**
* <p>Class {@code Ibs2Markers} stores the markers and intervals that are
* used to detect IBS2 segments.</p>
*
* <p>Instances of {@code Ibs2Markers} are immutable.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public final class Ibs2Markers {
private static final float MAX_MISS_FREQ = 0.1f;
private static final float MIN_MINOR_FREQ = 0.1f;
private static final int MIN_MARKER_CNT = 50;
private static final float MIN_INTERMARKER_CM = 0.02f;
private final Boolean[] useMarker;
private final IntArray stepStarts;
/**
* Constructs a new {@code Ibs2Markers} instance from the specified data.
*
* @param targGT target genotype data
* @param map a list whose {@code j}-th element is the genetic map position
* of the {@code j}-th the marker
* @param maf a list whose {@code j}-th element is the estimated minor
* allele frequency of the {@code j}-th the marker
* @throws IllegalArgumentException if
* {@code targGT.nMarkers() != map.genPos().size()}
* @throws IllegalArgumentException if {@code targGT.nMarkers() != maf.size()}
* @throws NullPointerException if
* {@code (targGT == null || map == null || maf == null)}
*/
public Ibs2Markers(GT targGT, MarkerMap map, FloatArray maf) {
if (map.genPos().size()!=targGT.nMarkers()) {
throw new IllegalArgumentException(
String.valueOf(map.genPos().size()));
}
if (maf.size()!=targGT.nMarkers()) {
throw new IllegalArgumentException(String.valueOf(maf.size()));
}
int maxMiss = (int) Math.ceil(MAX_MISS_FREQ*targGT.nHaps());
Boolean[] useMarker0 = IntStream.range(0, targGT.nMarkers())
.parallel()
.mapToObj(m -> useMarker(targGT, m, maf, maxMiss))
.toArray(Boolean[]::new);
this.stepStarts = stepStarts(useMarker0, map);
this.useMarker = useMarker0;
}
private static Boolean useMarker(GT targGT, int m, FloatArray maf,
int maxMissCnt) {
int missCnt = 0;
if (maf.get(m)>=MIN_MINOR_FREQ) {
for (int h=0, n=targGT.nHaps(); h<n; ++h) {
if (targGT.allele(m, h)<0) {
++missCnt;
}
}
return missCnt<=maxMissCnt;
}
else {
return false;
}
}
private static IntArray stepStarts(Boolean[] useMarker0, MarkerMap map) {
DoubleArray genPos = map.genPos();
int nMarkers = genPos.size();
IntList indices = new IntList(genPos.size()>>6);
int lastStart = 0;
int nextStart = nextStart(genPos, lastStart, useMarker0);
// following code combines the last two steps
while (nextStart<nMarkers) {
indices.add(lastStart);
lastStart = nextStart;
nextStart = nextStart(genPos, nextStart, useMarker0);
}
return new WrappedIntArray(indices);
}
private static int nextStart(DoubleArray genPos, int start,
Boolean[] useMarker0) {
double cmPos = genPos.get(start);
double minCmPos = cmPos + MIN_INTERMARKER_CM;
int nextStart = start + 1;
int mkrCnt = 0;
while (nextStart<useMarker0.length && mkrCnt<MIN_MARKER_CNT) {
if (useMarker0[nextStart]) {
cmPos = genPos.get(nextStart);
if (cmPos<minCmPos) {
useMarker0[nextStart] = Boolean.FALSE;
}
else {
++mkrCnt;
minCmPos = cmPos + MIN_INTERMARKER_CM;
}
}
++nextStart;
}
return nextStart;
}
/**
* Returns the number of markers.
* @return the number of markers
*/
public int nMarkers() {
return useMarker.length;
}
/**
* Returns an increasing list of marker indices that are used to detect
* IBS2 segments in the specified interval
* @param start the first marker in the interval (inclusive)
* @param end the last marker in the interval (exclusive)
* @return an increasing list of marker indices that are used to detect
* IBS2 segments in the specified interval
* @throws IllegalArgumentException if
* {@code start < 0 || end < start || end > this.nMarkers}
*/
public int[] markers(int start, int end) {
if (start<0 || end>useMarker.length) {
throw new IllegalArgumentException(String.valueOf(start));
}
if (end>useMarker.length) {
throw new IllegalArgumentException(String.valueOf(end));
}
IntList markers = new IntList(end - start);
for (int m=start; m<end; ++m) {
if (useMarker[m]) {
markers.add(m);
}
}
return markers.toArray();
}
/**
* Returns the first marker index in each step in increasing order.
* @return the first marker index in each step
*/
public IntArray stepStarts() {
return stepStarts;
}
}
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