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#include "PbbamInternalConfig.h"
#include "KSeqReader.h"
#include "ErrnoReason.h"
#include <sstream>
#include <stdexcept>
#include <vector>
#include <cassert>
namespace PacBio {
namespace BAM {
KSeqReader::KSeqReader(const std::string& fn)
: fp_{gzopen(fn.c_str(), "r")}, seq_{kseq_init(fp_.get())}
{
// check file handle
if (fp_ == nullptr) {
std::ostringstream msg;
msg << "[pbbam] kseq FASTX reader ERROR: could not open file:\n"
<< " file: " << fn << '\n';
MaybePrintErrnoReason(msg);
throw std::runtime_error{msg.str()};
}
// check kseq sequence handle
assert(seq_ != nullptr);
}
KSeqReader::KSeqReader(KSeqReader&&) noexcept = default;
KSeqReader& KSeqReader::operator=(KSeqReader&&) noexcept = default;
KSeqReader::~KSeqReader() = default;
std::string KSeqReader::Bases() const { return std::string{seq_->seq.s, seq_->seq.l}; }
std::string KSeqReader::Name() const { return std::string{seq_->name.s, seq_->name.l}; }
std::string KSeqReader::Qualities() const { return std::string{seq_->qual.s, seq_->qual.l}; }
bool KSeqReader::ReadNext()
{
const auto result = kseq_read(seq_.get());
if (result == -1) { // EOF
return false;
}
return true;
}
} // namespace BAM
} // namespace PacBio
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