LRA/Read.h at master · ChaissonLab/LRA · GitHub

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#ifndef READ_H_
#define READ_H_

#include <cstring>
using namespace std;
class Read {
 public:
	char *seq;
	char *qual;
	int  length;

	char *passthrough;
	string name;
	int flags;
	bool unaligned;
	void Clear() {
		if (seq != NULL) {
			delete[] seq;
			seq=NULL;
		}
		if (qual != NULL) {
			delete[] qual;
			qual=NULL;
		}
		if (passthrough != NULL) {
			delete[] passthrough;
			passthrough=NULL;
		}
		length=0;
		name="";
	}
	Read() {
		seq=NULL;
		length=0;
		qual=NULL;
		name="";
		passthrough=NULL;
		flags=0;
		unaligned=0;
	}
	Read(char* _sq, int _len, string _name, char*_qual=NULL) {
		seq=_sq;
		length=_len;
		qual=_qual;
		passthrough=NULL;
		name=_name;
		unaligned=0;
	}
	Read& operator=(const Read& rhs) {
		length=rhs.length;
		seq = NULL;
		qual= NULL;
		unaligned=0;
		if (rhs.length > 0) {
			if (rhs.seq != NULL) {
				seq = new char[length];
				memcpy(seq, rhs.seq, length);
			}
			if (rhs.qual != NULL) {
				int qualLen=strlen(rhs.qual);
				qual = new char[qualLen+1];
				memcpy(qual, rhs.qual, qualLen);
				qual[qualLen] = '\0';
			}
		}
		if (rhs.passthrough != NULL) {
			passthrough=new char[strlen(rhs.passthrough)];
			memcpy(passthrough, rhs.passthrough, strlen(rhs.passthrough));
		}

		name=rhs.name;
		return *this;
	}
};

#endif