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#include <seqan/bam_io.h>
using namespace seqan2;
int main()
{
CharString bamFileName = getAbsolutePath("demos/tutorial/sam_and_bam_io/example.sam");
// Open input file.
BamFileIn bamFileIn;
if (!open(bamFileIn, toCString(bamFileName)))
{
std::cerr << "ERROR: Could not open " << bamFileName << std::endl;
return 1;
}
unsigned numUnmappedReads = 0;
try
{
// Read header.
BamHeader header;
readHeader(header, bamFileIn);
// Read records.
BamAlignmentRecord record;
while (!atEnd(bamFileIn))
{
readRecord(record, bamFileIn);
if (hasFlagUnmapped(record))
numUnmappedReads += 1;
}
}
catch (Exception const & e)
{
std::cout << "ERROR: " << e.what() << std::endl;
return 1;
}
std::cout << "Number of unmapped reads: " << numUnmappedReads << "\n";
return 0;
}
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