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#include <seqan/bed_io.h>
#include <seqan/misc/name_store_cache.h>
using namespace seqan2;
int main()
{
// Open input bed file.
BedFileIn bedIn;
if (!open(bedIn, toCString(getAbsolutePath("demos/tutorial/bed_io/example.bed"))))
{
std::cerr << "ERROR: Could not open example.bed\n";
return 1;
}
// Array of counters and sequence names.
String<unsigned> counters;
StringSet<CharString> seqNames;
NameStoreCache<StringSet<CharString> > cache(seqNames);
// Read the file record by record.
BedRecord<Bed3> record;
try
{
while (!atEnd(bedIn))
{
readRecord(record, bedIn);
unsigned rID = nameToId(cache, record.ref);
// Resize counters if necessary and increment counter.
assignValueById(counters, rID, getValueById(counters, rID) + 1);
}
}
catch (Exception const & e)
{
std::cout << "ERROR: " << e.what() << std::endl;
return 1;
}
// Print result.
std::cout << "RECORDS ON CONTIGS\n";
for (unsigned i = 0; i < length(seqNames); ++i)
if (counters[i] != 0u)
std::cout << seqNames[i] << '\t' << counters[i] << '\n';
return 0;
}
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