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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 ints.IntArray;
import ints.SynchedIntList;
import java.util.Arrays;
import java.util.concurrent.atomic.AtomicReferenceArray;
import java.util.stream.IntStream;
import vcf.BasicGT;
import vcf.GTRec;
import vcf.Markers;
import vcf.RefGTRec;
import vcf.Samples;
import vcf.Window;
/**
* <p>Class {@code Stage2Haps} stores phased genotypes.</p>
*
* <p>Instances of {@code Stage2Haps} are thread-safe.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public class Stage2Haps {
private final FixedPhaseData fpd;
private final GTRec[] stage1Recs;
private final Markers markers;
private final Samples targSamples;
private final AtomicReferenceArray<SynchedIntList> rareCarriers;
/**
* Constructs a new {@code Stage2Haps} instance from the specified data.
* @param phaseData the current genotype phase estimates and parameter
* values
* @throws NullPointerException if {@code phaseData == null}
*/
public Stage2Haps(PhaseData phaseData) {
this.fpd = phaseData.fpd();
this.stage1Recs = phaseData.estPhase().toGTRecs();
this.markers = fpd.targGT().markers();
this.targSamples = fpd.targGT().samples();
this.rareCarriers = rareCarriers(fpd);
}
private static AtomicReferenceArray<SynchedIntList> rareCarriers(
FixedPhaseData fpd) {
int size = fpd.targGT().markers().sumAlleles();
AtomicReferenceArray<SynchedIntList> rareAlToHaps
= new AtomicReferenceArray<>(size);
IntStream.rangeClosed(0, fpd.stage1To2().size())
.parallel()
.forEach(j -> initList(fpd, j, rareAlToHaps));
return rareAlToHaps;
}
private static void initList(FixedPhaseData fpd, int index,
AtomicReferenceArray<SynchedIntList> rareCarriers) {
Markers markers = fpd.targGT().markers();
IntArray stage1To2 = fpd.stage1To2();
int start = index==0 ? 0 : stage1To2.get(index-1)+1;
int end = index==stage1To2.size() ? markers.size() : stage1To2.get(index);
for (int m=start; m<end; ++m) {
int nAlleles = markers.marker(m).nAlleles();
int offset = markers.sumAlleles(m);
for (int al=0; al<nAlleles; ++al) {
IntArray ia = fpd.carriers(m, al);
if (ia!=Window.HIGH_FREQ_ARRAY) {
rareCarriers.set(offset+al, new SynchedIntList(ia.size()));
}
}
}
}
/**
* 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 phased genotype if the specified marker was not phased
* in the first stage. The contract for this method is unspecified if the
* specified alleles are inconsistent with {@code this.fpd().targGT()}.
* @param sample a sample index
* @param marker a marker index
* @param a1 the first allele index
* @param a2 the second allele index
* @throws IndexOutOfBoundsException if
* {@code marker < 0 || marker >= this.fpd().targGT().markers().size()}
* @throws IndexOutOfBoundsException if
* {@code sample < 0 || sample >= this.fpd().targGT().samples().size()}
* @throws IndexOutOfBoundsException if
* {@code a1 < 0 || a1 >= this.fpd().targGT().markers().marker(marker).nAlleles()}
* @throws IndexOutOfBoundsException if
* {@code a2 < 0 || a2 >= this.fpd().targGT().markers().marker(marker).nAlleles()}
*/
public void setPhasedGT(int marker, int sample, int a1, int a2) {
int offset = markers.sumAlleles(marker);
SynchedIntList list1 = rareCarriers.get(offset + a1);
if (list1!=null) {
list1.add(sample<<1);
}
SynchedIntList list2 = rareCarriers.get(offset + a2);
if (list2!=null) {
list2.add((sample<<1) | 0b1);
}
}
/**
* Returns a {@code BasicGT} instance containing phased genotypes for
* the specified markers.
* @param start the starting marker index (inclusive)
* @param end the ending marker index (exclusive)
* @return a {@code BasicGT} instance containing phased genotypes for
* the specified range of marker indices
*
* @throws IndexOutOfBoundsException if
* {@code start < 0 || end > this.nMarkers()}
* @throws IllegalArgumentException if {@code start >= end}
*/
public BasicGT toBasicGT(int start, int end) {
GTRec[] recs = toGTRecs(start, end);
if (start==0 && end==markers.size()) {
return new BasicGT(markers, targSamples, recs);
}
else {
return new BasicGT(targSamples, recs);
}
}
/**
* Returns a {@code GTRec[]} instance containing phased genotypes for
* the specified markers.
* @param start the starting marker index (inclusive)
* @param end the ending marker index (exclusive)
* @return a {@code GTRec[]} instance containing phased genotypes for
* the specified range of marker indices
*
* @throws IndexOutOfBoundsException if
* {@code start < 0 || end > this.nMarkers()}
* @throws IllegalArgumentException if {@code start >= end}
*/
public GTRec[] toGTRecs(int start, int end) {
return IntStream.range(start, end)
.parallel()
.mapToObj(m -> gtRec(m))
.toArray(GTRec[]::new);
}
private GTRec gtRec(int m) {
int m1 = fpd.prevStage1Marker(m);
int m2 = fpd.stage1To2().get(m1);
return m==m2 ? stage1Recs[m1] : stage2Rec(m);
}
private RefGTRec stage2Rec(int m) {
int alStart = markers.sumAlleles(m);
int alEnd = markers.sumAlleles(m+1);
int[][] hapIndices = new int[alEnd - alStart][];
int majorAllele = -1;
for (int j=0; j<hapIndices.length; ++j) {
SynchedIntList list = rareCarriers.get(alStart + j);
if (list!=null) {
hapIndices[j] = list.toArray();
Arrays.sort(hapIndices[j]);
}
else {
majorAllele = j;
}
}
if (majorAllele == -1) { // can occur if all alleles are rare due to high missing rate
setMajorAlleleToNull(hapIndices);
}
return RefGTRec.alleleRefGTRec(markers.marker(m), targSamples, hapIndices);
}
private int setMajorAlleleToNull(int[][] hapIndices) {
int majAllele = 0;
for (int j=1; j<hapIndices.length; ++j) {
if (hapIndices[j].length > hapIndices[majAllele].length) {
majAllele = j;
}
}
hapIndices[majAllele] = null;
return majAllele;
}
}
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