private:
bool abort;
- string qualfile, outputDir, namefile;
+ string qualfile, outputDir, namefile, countfile;
vector<string> outputNames;
map<string, int> nameMap;
int processors;
vector<int> position;
vector<int> averageQ;
vector< vector<int> > scores;
- string filename, namefile;
+ string filename;
unsigned long long start;
unsigned long long end;
int count;
MothurOut* m;
+ bool hasNameMap;
map<string, int> nameMap;
~seqSumQualData(){}
- seqSumQualData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, string n, map<string, int> nam) {
+ seqSumQualData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, bool n, map<string, int> nam) {
filename = f;
m = mout;
start = st;
end = en;
- namefile = n;
+ hasNameMap = n;
nameMap = nam;
count = 0;
}
if (current.getName() != "") {
int num = 1;
- if (pDataArray->namefile != "") {
+ if (pDataArray->hasNameMap) {
//make sure this sequence is in the namefile, else error
map<string, int>::iterator it = pDataArray->nameMap.find(current.getName());