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/*
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"(
usage: vcfcat [file1] [file2] ... [fileN]
Concatenates VCF files
Type: transformation
)";
}
exit(1);
}
if (argc == 1) {
return 0;
} else {
for (int i = 1; i < argc; ++i) {
VariantCallFile variantFile;
string filename = argv[i];
variantFile.open(filename);
if (!variantFile.is_open()) {
cerr << "could not open " << argv[i] << endl;
return 1;
}
if (i == 1) {
cout << variantFile.header << endl;
}
Variant var(variantFile);
while (variantFile.getNextVariant(var)) {
cout << var << endl;
}
}
}
return 0;
}
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