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#ifndef __OUTPUT_UNMAPPED_FILTER_HPP__
#define __OUTPUT_UNMAPPED_FILTER_HPP__
#include <iostream>
#include <tbb/concurrent_queue.h>
#include "UnpairedRead.hpp"
#include "ReadPair.hpp"
template <typename FragT>
class OutputUnmappedFilter {
public:
OutputUnmappedFilter(tbb::concurrent_bounded_queue<FragT*>* outQueue) :
outQueue_(outQueue), qlen_(0) {
memset(&qname_[0], 0, 255);
}
inline void processFrag(FragT* f) {
bool distinctRead{true};
// Check if the new read name is distinct from
// the previous one.
auto newLen = f->getNameLength();
if (qlen_ == newLen) {
distinctRead = (memcmp(&qname_[0], f->getName(), qlen_) != 0);
}
// If this doesn't have the same name as the last read we saw,
// than pass it to the output queue and update the name of the
// most recently observed read.
if (distinctRead) {
auto* alnCpy = f->clone();
outQueue_->push(alnCpy);
qlen_ = newLen;
memcpy(&qname_[0], f->getName(), qlen_);
}
// If it does have the same name as the last read, no need
// to update.
}
private:
tbb::concurrent_bounded_queue<FragT*>* outQueue_ = nullptr;
char qname_[255];
uint32_t qlen_;
};
#endif // __OUTPUT_UNMAPPED_FILTER_HPP__
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