PairedEndRead.h

#ifndef PAIREDENDREAD
#define PAIREDENDREAD

#include<cassert>
#include<iostream>
#include<string>

#include "Read.h"
#include "SingleRead.h"

class PairedEndRead : public Read {
public:
	PairedEndRead() : mate1(), mate2() {}
	PairedEndRead(const SingleRead& mate1, const SingleRead& 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 SingleRead& getMate1() const { return mate1; }
	const SingleRead& getMate2() const { return mate2; }
	const SingleRead& 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:
	SingleRead mate1, mate2;
};

bool PairedEndRead::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 PairedEndRead::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 PairedEndRead::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