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#include <seqan/basic.h>
#include <seqan/bed_io.h>
using namespace seqan;
// USAGE: bed_stream_read IN.bed
//
// Read BED file and print the positions (reference, position) to stdout.
//
// We only read BED 3 here but the example can be easily adjusted to more complex examples.
int main(int argc, char const * argv[])
{
if (argc != 2)
{
std::cerr << "USAGE: " << argv[0] << " IN.bed\n";
return 1;
}
BedFileIn bedIn;
if (!open(bedIn, argv[1]))
{
std::cerr << "ERROR: Could not open " << argv[1] << " for reading!\n";
return 1;
}
BedRecord<Bed3> record;
while (!atEnd(bedIn))
{
readRecord(record, bedIn);
std::cout << record.ref << "\t" << record.beginPos << "\n";
}
return 0;
}
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