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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 java.util.concurrent.atomic.AtomicReferenceArray;
import vcf.BitArrayRefGTRec;
import vcf.XRefGT;
/**
* <p>Class {@code EstPhase} stores input genotype data and the
* current estimated phased genotypes for each target sample.</p>
*
* <p>Instances of class {@code EstPhase} are thread-safe.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public final class EstPhase {
private final FixedPhaseData fpd;
private final AtomicReferenceArray<SamplePhase> phase;
/**
* Constructs a new {@code EstPhase} instance from the specified data.
* @param fpd the input data for phasing
* @param seed the seed for random number generation
* @throws NullPointerException if {@code fpd == null}
*/
public EstPhase(FixedPhaseData fpd, long seed) {
this.fpd = fpd;
this.phase = PbwtPhaser.initPhase(fpd, seed);
}
/**
* Returns the input data for phasing that is the same in each iteration.
* @return the input data for phasing that is the same in each iteration
*/
public FixedPhaseData fpd() {
return fpd;
}
/**
* Sets the specified phased genotypes for the specified sample.
* @param sample the sample index
* @param samplePhase the estimated phased genotypes
* @throws IndexOutOfBoundsException if
* {@code sample < 0 || sample >= this.fpd().stage1TargGT().nSamples()}
* @throws NullPointerException if {@code samplePhase == null}
*/
public void set(int sample, SamplePhase samplePhase) {
if (samplePhase==null) {
throw new NullPointerException(SamplePhase.class.toString());
}
phase.set(sample, samplePhase);
}
/**
* Return the estimated phase for the specified sample.
* @param sample a sample index
* @return the estimated phase for the specified sample
* @throws IndexOutOfBoundsException if
* {@code sample < 0 || sample >= this.fpd().targGT().nSamples()}
*/
public SamplePhase get(int sample) {
return phase.get(sample);
}
/**
* Returns the current estimated phased genotypes for the target samples.
* @return the current estimated phased genotypes for the target samples
*/
public XRefGT phasedHaps() {
return XRefGT.from(fpd.stage1TargGT().samples(), phase);
}
/**
* Returns the current estimated phased genotypes for the target samples.
* @return the current estimated phased genotypes for the target samples
*/
public BitArrayRefGTRec[] toGTRecs() {
return BitArrayRefGTRec.toBitArrayRefGTRecs(this);
}
}
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