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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;
import blbutil.BitArray;
import java.util.stream.IntStream;
/**
* <p>Class {@code BitArrayGT} represents genotypes for a list of samples
* at a single marker. Instances of class {@code BitArrayGTRec} store
* haplotype alleles and flags to indicate missing genotypes in bit sets. All
* genotypes are considered to be unphased if any sample has an
* unphased or missing genotype.t</p>
*
* <p>Instances of class {@code BitArrayGTRec} are immutable.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public final class BitArrayGTRec implements GTRec {
private final int bitsPerAllele;
private final Marker marker;
private final Samples samples;
private final boolean isPhased;
private final BitArray isMissing;
private final BitArray alleles;
/**
* Constructs a new {@code BitArrayGT} instance representing
* the specified VCF record's GT format field data.
*
* @param recParser the VCF record genotype data
* @throws IllegalArgumentException if a format error is detected
* in the VCF record
* @throws NullPointerException if {@code recParser == null}
*/
public BitArrayGTRec(VcfRecGTParser recParser) {
int nSamples = recParser.samples().size();
int nHaps = nSamples<<1;
this.bitsPerAllele = recParser.marker().bitsPerAllele();
this.marker = recParser.marker();
this.samples = recParser.samples();
BitArray alleleList = new BitArray(nHaps*bitsPerAllele);
BitArray isMissingList = new BitArray(nSamples);
this.isPhased = recParser.storeAlleles(alleleList, isMissingList);
this.isMissing = isMissingList;
this.alleles = alleleList;
}
/**
* Constructs a new {@code BitArrayGT} instance representing
* the specified VCF record's GT format field data.
*
* @param hlr the VCF record genotype data
* @throws IllegalArgumentException if a format error is detected
* in the VCF record
* @throws NullPointerException if {@code hlr == null}
*/
public BitArrayGTRec(VcfRecGTParser.HapListRep hlr) {
int nSamples = hlr.samples().size();
int nHaps = nSamples<<1;
this.bitsPerAllele = hlr.marker().bitsPerAllele();
this.marker = hlr.marker();
this.samples = hlr.samples();
this.isPhased = hlr.isPhased();
this.isMissing = new BitArray(nSamples);
this.alleles = new BitArray(nHaps*bitsPerAllele);
boolean setMajorToNull = false;
int[][] hapLists = hlr.hapLists(setMajorToNull);
int[] missingSamples = hlr.missingSamples();
for (int al=0; al<hapLists.length; ++al) {
int[] list = hapLists[al];
for (int h : list) {
storeAllele(alleles, h, bitsPerAllele, al);
}
}
for (int s : missingSamples) {
isMissing.set(s);
}
}
private static void storeAllele(BitArray alleles, int hap, int bitsPerAllele,
int allele) {
int index = hap*bitsPerAllele;
int mask = 1;
for (int k=0; k<bitsPerAllele; ++k) {
if ((allele & mask)==mask) {
alleles.set(index);
}
++index;
mask <<= 1;
}
}
@Override
public Samples samples() {
return samples;
}
@Override
public int size() {
return 2*samples.size();
}
@Override
public Marker marker() {
return marker;
}
@Override
public boolean isPhased() {
return isPhased;
}
@Override
public boolean isPhased(int sample) {
return isPhased;
}
@Override
public int allele1(int sample) {
return isMissing.get(sample) ? -1 : allele(sample<<1);
}
@Override
public int allele2(int sample) {
return isMissing.get(sample) ? -1 : allele((sample<<1) | 0b1);
}
@Override
public int get(int hap) {
return isMissing.get(hap>>1) ? -1 : allele(hap);
}
private int allele(int hap) {
int start = bitsPerAllele*hap;
int end = start + bitsPerAllele;
int allele = 0;
int mask = 1;
for (int j=start; j<end; ++j) {
if (alleles.get(j)) {
allele += mask;
}
mask <<= 1;
}
return allele;
}
@Override
public int[] alleles() {
return IntStream.range(0, size())
.map(h -> get(h))
.toArray();
}
/**
* Returns the data represented by {@code this} as a VCF
* record with a GT format field. The returned VCF record
* will have missing QUAL and INFO fields, will have "PASS"
* in the filter field, and will have a GT format field.
* @return the data represented by {@code this} as a VCF
* record with a GT format field
*/
@Override
public String toString() {
return GTRec.toVcfRec(this);
}
}
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