1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
|
/*
* 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;
import phase.EstPhase;
import phase.SamplePhase;
/**
* <p>Class {@code BitArrayRefGTRec} represents phased, nonmissing, genotypes
* for a list of samples at a single marker. Instances of class
* {@code BitArrayRefGTRec} store haplotype alleles in bit sets.</p>
*
* <p>Instances of class {@code BitArrayRefGTRec} are immutable.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public final class BitArrayRefGTRec implements GTRec {
private final int bitsPerAllele;
private final Marker marker;
private final Samples samples;
private final BitArray alleles;
/**
* Returns the current estimated phased, non-missing genotypes. This
* method converts column-major data into row-major data.
* @param estPhase the current estimated phased genotypes for each target
* sample
* @return the current estimated phased, non-missing genotypes
* @throws NullPointerException if {@code estPhase == null}
*/
public static BitArrayRefGTRec[] toBitArrayRefGTRecs(EstPhase estPhase) {
GT gt = estPhase.fpd().stage1TargGT();
Markers markers = gt.markers();
Samples samples = gt.samples();
BitArray[] bitLists = SamplePhase.toBitLists(estPhase);
return IntStream.range(0, bitLists.length)
.parallel()
.mapToObj(m -> new BitArrayRefGTRec(markers.marker(m), samples, bitLists[m]))
.toArray(BitArrayRefGTRec[]::new);
}
// NB: The toBitArrayRefGTRecs() method is commented-out because it is
// not currently used
// ToDo: decide whether to delete toBitArrayRefGTRecs() method after
// XRefGT amd BrefGT code stabilizes.
//
// /**
// * Returns the phased, non-missing genotypes as a {@code BitArrayRefGTRec[]}
// * array. This method converts column-major data into row-major data.
// * @param gt the genotype data
// * @param nThreads the maximum number of computational threads for object
// * construction
// * @return the phased, non-missing genotypes as a {@code BitArrayRefGTRec[]}
// * array
// * @throws IllegalArgumentException if {@code nThreads < 1}
// * @throws NullPointerException if {@code gt == null}
// */
// public static BitArrayRefGTRec[] toBitArrayRefGTRecs(XRefGT gt, int nThreads) {
// Markers markers = gt.markers();
// Samples samples = gt.samples();
// BitArray[] bitLists = gt.toBitLists(nThreads);
// return IntStream.range(0, bitLists.length)
// .parallel()
// .mapToObj(m -> new BitArrayRefGTRec(markers.marker(m), samples, bitLists[m]))
// .toArray(BitArrayRefGTRec[]::new);
// }
private BitArrayRefGTRec(Marker marker, Samples samples, BitArray alleles) {
this.bitsPerAllele = marker.bitsPerAllele();
this.marker = marker;
this.samples = samples;
this.alleles = alleles;
}
@Override
public Samples samples() {
return samples;
}
@Override
public int size() {
return samples.size()<<1;
}
@Override
public Marker marker() {
return marker;
}
@Override
public boolean isPhased() {
return true;
}
@Override
public boolean isPhased(int sample) {
return true;
}
@Override
public int get(int hap) {
return 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;
}
/**
* 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);
}
}
|
