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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 imp;
import blbutil.Utilities;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.atomic.AtomicReferenceArray;
/**
* <p>Class {@code ImpLS} computes HMM state probabilities
* at genotyped markers in the target haplotypes.
* </p>
* <p>Instances of class {@code ImpLS} are thread-safe.
* </p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public final class ImpLS {
private ImpLS() {
// private constructor to prevent instantiation
}
/**
* Returns estimated HMM state probabilities at genotyped markers
* for each target haplotype. The returned array maps each target
* haplotype index to the target haplotype's HMM state probabilities.
* @param impData the input data for genotype imputation
* @return a list of HMM state probabilities at genotyped markers
* for each target haplotype.
* @throws NullPointerException if {@code impData == null}
*/
public static AtomicReferenceArray<StateProbs> stateProbs(ImpData impData) {
int nThreads = impData.par().nthreads();
int nTargHaps = impData.targGT().nHaps();
final AtomicReferenceArray<StateProbs> stProbs
= new AtomicReferenceArray<>(nTargHaps);
final AtomicInteger hapIndices = new AtomicInteger(0);
ExecutorService es = Executors.newFixedThreadPool(nThreads);
ImpIbs ibsHaps = new ImpIbs(impData);
try {
for (int j=0; j<nThreads; ++j) {
ImpLSBaum baum = new ImpLSBaum(impData, ibsHaps);
es.submit(() -> {
try {
int hap = hapIndices.getAndIncrement();
while (hap>=0 && hap<nTargHaps) {
StateProbs stateProbs = baum.impute(hap);
stProbs.set(hap, stateProbs);
hap = hapIndices.getAndIncrement();
}
}
catch(Throwable t) {
Utilities.exit(t);
}
} );
}
es.shutdown();
es.awaitTermination(Long.MAX_VALUE, TimeUnit.DAYS);
}
catch (Throwable t) {
Utilities.exit(t);
}
return stProbs;
}
}
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