Function countPattern

src/utils/sequenceUtilities/sequenceUtils.cpp:214–232

int countPattern(const string &seq, const string &pattern, bool ignoreCase)
{
    string s = seq;
    string p = pattern;
    // standardize the seq and the pattern 
    // if case should be ignored
    if (ignoreCase) {
        toUpperCase(s);
        toUpperCase(p);
    }
    int patternLength = p.size();
    int patternCount = 0;
    for(unsigned int i = 0; i < s.length(); i++) {
        if (s.substr(i,patternLength) == p) {
            patternCount++;
        }
    }
    return patternCount;
}