- public:
- SingleRead() { readseq = ""; len = 0; }
- SingleRead(const std::string& name, const std::string& readseq) {
- this->name = name;
- this->readseq = readseq;
- this->len = readseq.length();
- calc_lq();
- }
-
- bool read(int argc, std::istream* argv[], int flags = 7);
- void write(int argc, std::ostream* argv[]);
-
- const int getReadLength() const { return len; /*readseq.length();*/ } // If need memory and .length() are guaranteed O(1), use statement in /* */
- const std::string& getReadSeq() const { return readseq; }
-
- private:
- int len; // read length
- std::string readseq; // read sequence
-
- void calc_lq();
+public:
+ SingleRead() { readseq = ""; len = 0; }
+ SingleRead(const std::string& name, const std::string& readseq) {
+ this->name = name;
+ this->readseq = readseq;
+ this->len = readseq.length();
+ }
+
+ bool read(int argc, std::istream* argv[], int flags = 7);
+ void write(int argc, std::ostream* argv[]);
+
+ const int getReadLength() const { return len; /*readseq.length();*/ } // If need memory and .length() are guaranteed O(1), use statement in /* */
+ const std::string& getReadSeq() const { return readseq; }
+
+ void calc_lq(bool, int); // calculate if this read is low quality. Without calling this function, isLowQuality() will always be false
+
+private:
+ int len; // read length
+ std::string readseq; // read sequence