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
|
/*
vcflib C++ library for parsing and manipulating VCF files
Copyright © 2010-2020 Erik Garrison
Copyright © 2020 Pjotr Prins
This software is published under the MIT License. See the LICENSE file.
*/
#include "Variant.h"
using namespace std;
using namespace vcflib;
int main(int argc, char** argv) {
if (argc == 2) {
string h_flag = argv[1];
if (h_flag == "-h" || h_flag == "--help") {
cerr << R"(
Summarize by site
Usage: vcfsitesummarize <vcf file>
Example:
vcfsitesummarize samples/sample.vcf
CHROM POS ID REF QUAL FILTER AA AC AF AN DP NS DB H2
19 111 . A 9.6 . 0 0
19 112 . A 10 . 0 0
20 14370 rs6054257 G 29 PASS 0.5 14 3 1 1
20 17330 . T 3 q10 0.017 11 3 0 0
20 1110696 rs6040355 A 67 PASS T 10 2 1 0
20 1230237 . T 47 PASS T 13 3 0 0
20 1234567 microsat1 G 50 PASS G 6 9 3 0 0
20 1235237 . T 0 . 0 0
X 10 rsTest AC 10 PASS
Type: statistics
)";
exit(1);
}
}
VariantCallFile variantFile;
if (argc > 1) {
string filename = argv[1];
variantFile.open(filename);
} else {
variantFile.open(std::cin);
}
if (!variantFile.is_open()) {
return 1;
}
// obtain all possible field names
vector<string> infofields;
vector<string> infoflags;
for (map<string, VariantFieldType>::iterator i = variantFile.infoTypes.begin(); i != variantFile.infoTypes.end(); ++i) {
if (variantFile.infoCounts[i->first] != ALLELE_NUMBER) {
if (i->second == FIELD_BOOL) {
infoflags.push_back(i->first);
} else {
infofields.push_back(i->first);
}
}
}
// write header
// defaults
cout << "CHROM\tPOS\tID\tREF\tQUAL\tFILTER";
// configurable info field
for (vector<string>::iterator i = infofields.begin(); i != infofields.end(); ++i) {
cout << "\t" << *i;
}
for (vector<string>::iterator i = infoflags.begin(); i != infoflags.end(); ++i) {
cout << "\t" << *i;
}
cout << endl;
Variant var(variantFile);
while (variantFile.getNextVariant(var)) {
cout << var.sequenceName << "\t"
<< var.position << "\t"
<< var.id << "\t"
<< var.ref << "\t"
<< var.quality << "\t"
<< var.filter;
for (vector<string>::iterator i = infofields.begin(); i != infofields.end(); ++i) {
vector<string> value;
string& name = *i;
map<string, vector<string> >::iterator f = var.info.find(name);
if (f != var.info.end()) {
value = f->second;
if (value.size() == 1) {
cout << "\t" << value.front();
} else {
cout << "\t"; // null
}
} else {
cout << "\t"; // null
}
}
for (vector<string>::iterator i = infoflags.begin(); i != infoflags.end(); ++i) {
string value;
string& name = *i;
map<string, bool>::iterator f = var.infoFlags.find(name);
cout << "\t";
if (f != var.infoFlags.end()) {
cout << 1;
} else {
cout << 0;
}
}
cout << endl;
}
return 0;
}
|
