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#include <seqan/vcf_io.h>
using namespace seqan;
int main()
{
try
{
// Open input file.
VcfFileIn vcfIn(toCString(getAbsolutePath("demos/tutorial/vcf_io/example.vcf")));
// Copy over header.
VcfHeader header;
readHeader(header, vcfIn);
// Get array of counters.
String<unsigned> counters;
unsigned contigsCount = length(contigNames(context(vcfIn)));
resize(counters, contigsCount, 0);
// Read the file record by record.
VcfRecord record;
while (!atEnd(vcfIn))
{
readRecord(record, vcfIn);
// Register record with counters.
counters[record.rID] += 1;
}
// Print result.
std::cout << "VARIANTS ON CONTIGS\n";
for (unsigned i = 0; i < contigsCount; ++i)
std::cout << contigNames(context(vcfIn))[i] << '\t'
<< counters[i] << '\n';
}
catch (seqan::Exception const & e)
{
std::cerr << "ERROR:" << e.what() << std::endl;
return 1;
}
return 0;
}
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