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
|
/*
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"
#include "split.h"
#include <string>
#include <sstream>
#include <iostream>
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 << "usage: " << argv[0] << " <vcf file>" << endl << endl
<< "outputs a VCF stream where NUMALT has been generated for each record using sample genotypes" << endl;
cerr << endl << "Type: transformation" << endl << endl;
return 1;
}
}
string filename = argv[1];
VariantCallFile variantFile;
if (filename == "-") {
variantFile.open(std::cin);
} else {
variantFile.open(filename);
}
if (!variantFile.is_open()) {
cerr << "could not open " << filename << endl;
return 1;
}
Variant var(variantFile);
// remove header lines we're going to add
variantFile.removeInfoHeaderLine("NUMALT");
// and add them back, so as not to duplicate them if they are already there
variantFile.addHeaderLine("##INFO=<ID=NUMALT,Number=1,Type=Integer,Description=\"Total number of segregating alternate alleles at the loci\">");
// write the new header
cout << variantFile.header << endl;
// print the records, filtering is done via the setting of varA's output sample names
while (variantFile.getNextVariant(var)) {
stringstream na;
na << var.alt.size();
var.info["NUMALT"].clear();
var.info["NUMALT"].push_back(na.str());
cout << var << endl;
}
return 0;
}
|
