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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;
/**
* <p>Class {@code SplicedGT} represents genotypes for a set of samples
* that are obtained by replacing the initial markers of one {@code GT}
* instance with phased genotypes from another {@code GT} instance.
* </p>
* <p>Instances of class {@code SplicedGT} are immutable.
* </p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public final class SplicedGT implements GT {
private final int overlap;
private final GT phasedGT;
private final GT gt;
/**
* Constructs a new {@code SplicedGL} instance.
* @param phasedOverlap sample haplotype pairs for the initial
* markers
* @param gt genotype emission probabilities for all markers
* @throws IllegalArgumentException if
* {@code phasedOverlaps.nMarkers() >= gt.nMarkers()}
* @throws IllegalArgumentException if
* {@code phasedOverlaps.marker(j).equals(gt.marker(j)) == false} for any {@code j}
* satisfying {@code 0 <= j && j < phasedOverlaps.nMarkers()}
* @throws IllegalArgumentException if
* {@code phasedOverlaps.samples().equals(gt.samples()) == false}
* @throws IllegalArgumentException if
* {@code phasedOverlap.isPhased() == false}
* @throws NullPointerException if
* {@code phasedOverlap == null || gt == null}
*/
public SplicedGT(GT phasedOverlap, GT gt) {
if (phasedOverlap.nMarkers()>=gt.nMarkers()) {
throw new IllegalArgumentException("inconsistent markers");
}
for (int j=0, n=phasedOverlap.nMarkers(); j<n; ++j) {
if (phasedOverlap.marker(j).equals(gt.marker(j))==false) {
throw new IllegalArgumentException("inconsistent markers");
}
}
if (phasedOverlap.samples().equals(gt.samples())==false) {
throw new IllegalArgumentException("inconsistent samples");
}
this.overlap = phasedOverlap.nMarkers();
this.phasedGT = phasedOverlap;
this.gt = gt;
}
@Override
public boolean isReversed() {
return false;
}
@Override
public Marker marker(int marker) {
return gt.marker(marker);
}
@Override
public Markers markers() {
return gt.markers();
}
@Override
public int nMarkers() {
return gt.nMarkers();
}
@Override
public int nHaps() {
return gt.nHaps();
}
@Override
public int nSamples() {
return gt.nSamples();
}
@Override
public Samples samples() {
return gt.samples();
}
@Override
public boolean isPhased() {
return gt.isPhased();
}
@Override
public int allele1(int marker, int sample) {
if (marker<overlap) {
return phasedGT.allele1(marker, sample);
}
else {
return gt.allele1(marker, sample);
}
}
@Override
public int allele2(int marker, int sample) {
if (marker<overlap) {
return phasedGT.allele2(marker, sample);
}
else {
return gt.allele2(marker, sample);
}
}
@Override
public int allele(int marker, int hap) {
if (marker<overlap) {
return phasedGT.allele(marker, hap);
}
else {
return gt.allele(marker, hap);
}
}
@Override
public GT restrict(Markers markers, int[] indices) {
return new RestrictedGT(this, markers, indices);
}
@Override
public GT restrict(int start, int end) {
if (start>=overlap) {
return gt.restrict(start, end);
}
else {
GT restrictPhasedGT = phasedGT.restrict(start, overlap);
GT restrictGT = gt.restrict(start, end);
return new SplicedGT(restrictPhasedGT, restrictGT);
}
}
@Override
public String toString() {
StringBuilder sb = new StringBuilder(10000);
sb.append("SplicedGL: nSamples=");
sb.append(this.nSamples());
return sb.toString();
}
}
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