textLen_ is uninitialised in the function lce()

In RapMap v.0.5.0, textLen_ is uninitialised in the function lce() in the file include/SASearcher.hpp. The function in question is in the code snippet below.

        OffsetT lce(OffsetT p1, OffsetT p2,
                    OffsetT startAt=0,
                    OffsetT stopAt=std::numeric_limits<OffsetT>::max(),
                    bool verbose=false) {
            std::string& seq = *seq_;
            std::vector<OffsetT>& SA = *sa_;
            OffsetT len = static_cast<OffsetT>(startAt);
            auto o1 = SA[p1] + startAt;
            auto o2 = SA[p2] + startAt;
            auto maxIndex = std::max(o1, o2);
            while (maxIndex + len < textLen_ and seq[o1+len] == seq[o2+len]) {
                if (seq[o1+len] == '$') { break; }
                if (len >= stopAt) { break; }
                ++len;
            }
            return len;
        }

The value of textLen is never set. In practice, if I modify the function to print the value of textLen as below, I find that textLen is always zero, meaning the central while loop is never executed. This is also the case on the develop-salmon branch (although under default command line options, lce is never actually executed on this branch). I am guessing that the aim of the first condition of the while loop (maxIndex + len < textLen) is to stop the while loop from executing if we have reached the end of the transcriptome. If I am correct, this bug could be fixed by setting the value of textLen_ to the length of the transcriptome.


        OffsetT lce(OffsetT p1, OffsetT p2,
                    OffsetT startAt=0,
                    OffsetT stopAt=std::numeric_limits<OffsetT>::max(),
                    bool verbose=false) {

        std::cerr << "In lce" << '\n';
        std::cerr << "textLen_ = " << textLen_ << '\n';
            std::string& seq = *seq_;
            std::vector<OffsetT>& SA = *sa_;
            OffsetT len = static_cast<OffsetT>(startAt);
            auto o1 = SA[p1] + startAt;
            auto o2 = SA[p2] + startAt;
            auto maxIndex = std::max(o1, o2);
            while (maxIndex + len < textLen_ and seq[o1+len] == seq[o2+len]) {
                if (seq[o1+len] == '$') { break; }
                if (len >= stopAt) { break; }
                ++len;
            }
            return len;
        }

COMBINE-lab / RapMap

textLen_ is uninitialised in the function lce() #45