vector<string> setParameters();
string getCommandName() { return "summary.qual"; }
string getCommandCategory() { return "Sequence Processing"; }
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Summary.qual"; }
string getDescription() { return "summarize the quality of a set of sequences"; }
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;
+ int count, numSeqs;
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;
}
in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
}
- int count = 0;
+ pDataArray->count = 0;
+ pDataArray->numSeqs = 0;
for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
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());
else { pDataArray->scores.at(i)[thisScores[i]] += num; }
}
- count += num;
+ pDataArray->numSeqs += num;
+ pDataArray->count++;
}
}
- pDataArray->count = count;
in.close();
return 0;