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#ifndef PAIREDENDREADQ_H_
#define PAIREDENDREADQ_H_
#include<cassert>
#include<iostream>
#include<string>
#include "Read.h"
#include "SingleReadQ.h"
class PairedEndReadQ : public Read {
public:
PairedEndReadQ() : mate1(), mate2() {}
PairedEndReadQ(const SingleReadQ& mate1, const SingleReadQ& mate2) {
this->mate1 = mate1;
this->mate2 = mate2;
this->name = mate1.getName();
}
bool read(int argc, std::istream* argv[], int flags = 7);
void write(int argc, std::ostream* argv[]);
const SingleReadQ& getMate1() const { return mate1; }
const SingleReadQ& getMate2() const { return mate2; }
const SingleReadQ& getMate(int i) const {
if (i == 1) return mate1;
else return mate2;
}
void calc_lq(bool, int); // calculate if this read is low quality. Without calling this function, isLowQuality() will always be false
private:
SingleReadQ mate1, mate2;
};
bool PairedEndReadQ::read(int argc, std::istream* argv[], int flags) {
bool success;
std::istream *inpMate1[1], *inpMate2[1];
assert(argc == 2);
inpMate1[0] = argv[0]; inpMate2[0] = argv[1];
success = mate1.read(1, inpMate1, flags) && mate2.read(1, inpMate2, flags);
name = "";
if (flags & 4) { name = mate1.getName(); } //May chop 1 char later if we want
return success;
}
void PairedEndReadQ::write(int argc, std::ostream* argv[]) {
std::ostream *outMate1[1], *outMate2[1];
assert(argc == 2);
outMate1[0] = argv[0]; outMate2[0] = argv[1];
mate1.write(1, outMate1);
mate2.write(1, outMate2);
}
//calculate if this read is low quality
void PairedEndReadQ::calc_lq(bool hasPolyA, int seedLen) {
low_quality = false;
mate1.calc_lq(hasPolyA, seedLen);
mate2.calc_lq(hasPolyA, seedLen);
if (mate1.getReadLength() < seedLen || mate2.getReadLength() < seedLen) low_quality = true;
else low_quality = mate1.isLowQuality() && mate2.isLowQuality();
}
#endif /* PAIREDENDREADQ_H_ */
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