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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.Const;
import blbutil.MultiThreadUtils;
import blbutil.Utilities;
import java.util.Arrays;
import java.util.Random;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.IntStream;
import main.Par;
/**
* <p>Class {@code PhaseLS} contains static methods for estimated genotypes
* phase using a haploid Li and Stephens hidden Markov model.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public class PhaseLS {
private PhaseLS() {
// private constructor to prevent instantiation
}
/**
* Updates genotype phase estimates in the target samples.
* @param pd estimated phased genotypes at stage 1 markers
* @throws NullPointerException if {@code pd == null}
*/
public static void runStage1(PhaseData pd) {
Par par = pd.fpd().par();
int it = pd.it();
int nThreads = par.nthreads();
int nSamples = pd.fpd().targGT().nSamples();
int nBurninIts = par.burnin();
PbwtPhaseIbs phaseIbs = pbwtPhaseIbs(pd);
if (par.em()) {
Random rand = new Random(pd.seed());
if (it==0) {
initializeParameters(phaseIbs, rand);
}
else if (it<nBurninIts) {
updateParameters(phaseIbs, rand);
}
}
AtomicInteger samples = new AtomicInteger(0);
ExecutorService es = Executors.newFixedThreadPool(nThreads);
for (int j=0; j<nThreads; ++j) {
es.submit(() -> {
try {
PhaseBaum2 baum = new PhaseBaum2(phaseIbs);
for (int s=samples.getAndIncrement(); s<nSamples;
s=samples.getAndIncrement()) {
baum.phase(s);
}
}
catch (Throwable t) {
Utilities.exit(t);
}
} );
}
MultiThreadUtils.shutdownExecService(es);
}
private static PbwtPhaseIbs pbwtPhaseIbs(PhaseData pd) {
boolean useBwd = (pd.it() & 1)==0;
PbwtPhaseIbs phaseIbs = new PbwtPhaseIbs(pd, pd.codedSteps(), useBwd);
return phaseIbs;
}
private static void initializeParameters(PbwtPhaseIbs phaseIbs, Random rand) {
PhaseData pd = phaseIbs.phaseData();
float prevRecInt = pd.recombIntensity();
int maxInitialIts = 15;
for (int j=0; j<maxInitialIts; ++j) {
updateParameters(phaseIbs, rand);
float recInt = pd.recombIntensity();
if (Math.abs(recInt - prevRecInt) <= 0.1*prevRecInt) {
break;
}
prevRecInt = recInt;
}
}
private static void updateParameters(PbwtPhaseIbs phaseIbs, Random rand) {
ParamEstimates paramEst = getParamEst(phaseIbs, rand);
PhaseData pd = phaseIbs.phaseData();
float prevPMismatch = pd.pMismatch();
float pMismatch = paramEst.pMismatch();
float recombIntensity = paramEst.recombIntensity();
if (Float.isFinite(pMismatch) && pMismatch>prevPMismatch) {
pd.updatePMismatch(pMismatch);
}
if (Float.isFinite(recombIntensity) && recombIntensity>0f) {
pd.updateRecombIntensity(recombIntensity);
}
}
private static ParamEstimates getParamEst(PbwtPhaseIbs phaseIbs, Random rand) {
ParamEstimates paramEst = new ParamEstimates();
PhaseData pd = phaseIbs.phaseData();
FixedPhaseData fpd = pd.fpd();
int[] sampleIndices = samplesToAnalyze(pd, rand);
int nThreads = Math.min(fpd.par().nthreads(), sampleIndices.length);
double maxSum = 20000.0/nThreads;
int minIndices = 50;
AtomicInteger counter = new AtomicInteger(0);
ExecutorService es = Executors.newFixedThreadPool(nThreads);
for (int j=0; j<nThreads; ++j) {
es.submit(() -> {
try {
HmmParamData hpd = new HmmParamData(phaseIbs);
int index = counter.getAndIncrement();
while ((hpd.sumSwitchProbs()<maxSum || index<minIndices)
&& index<sampleIndices.length) {
hpd.update(sampleIndices[index]);
index = counter.getAndIncrement();
hpd.addEstimationData(paramEst);
}
}
catch (Throwable t) {
Utilities.exit(t);
}
} );
}
MultiThreadUtils.shutdownExecService(es);
return paramEst;
}
private static int[] samplesToAnalyze(PhaseData pd, Random rand) {
int maxSamplesToAnalyze = 500;
int nTargSamples = pd.fpd().targGT().nSamples();
int[] ia = IntStream.range(0, nTargSamples)
.parallel()
.toArray();
if (nTargSamples <= maxSamplesToAnalyze) {
return ia;
}
else {
Utilities.shuffle(ia, maxSamplesToAnalyze, rand);
return Arrays.copyOf(ia, maxSamplesToAnalyze);
}
}
/**
* Returns phased genotypes at all markers.
* @param pd estimated phased genotypes at stage 1 markers
* @return estimated phased genotypes at all markers
* @throws NullPointerException if {@code pd == null}
*/
public static Stage2Haps runStage2(PhaseData pd) {
FixedPhaseData fpd = pd.fpd();
int nThreads = fpd.par().nthreads();
int nSamples = fpd.targGT().nSamples();
LowFreqPhaseIbs phaseIbs = new LowFreqPhaseIbs(pd);
Stage2Haps stage2Haps = new Stage2Haps(pd);
AtomicInteger samples = new AtomicInteger(0);
ExecutorService es = Executors.newFixedThreadPool(nThreads);
for (int j=0; j<nThreads; ++j) {
es.submit(() -> {
try {
Stage2Baum baum = new Stage2Baum(phaseIbs, stage2Haps);
for (int s=samples.getAndIncrement(); s<nSamples;
s=samples.getAndIncrement()) {
baum.phase(s);
}
}
catch (Throwable t) {
Utilities.exit(t);
}
} );
}
MultiThreadUtils.shutdownExecService(es);
return stage2Haps;
}
}
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