out2 << it->first << '\t' << it->second << endl;
}
out2.close();
-
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
out << querySeq->getName() << endl << endl << "Reference sequences used and distance to query:" << endl;
for (int j = 0; j < closest.size(); j++) {
- out << setprecision(3) << closest[j].seq->getName() << '\t' << closest[j].dist << endl;
+ out << closest[j].seq->getName() << '\t' << closest[j].dist << endl;
}
out << endl << endl;
out << endl << "Window\tStartPos\tEndPos" << endl;
it = trim.begin();
-
for (int k = 0; k < windows.size()-1; k++) {
out << k+1 << '\t' << spotMap[windows[k]-it->first] << '\t' << spotMap[windows[k]-it->first+windowSizes] << endl;
}
out << windows.size() << '\t' << spotMap[windows[windows.size()-1]-it->first] << '\t' << spotMap[it->second-it->first-1] << endl;
out << endl;
-
out << "Window\tAvgQ\t(sdQ)\tAvgR\t(sdR)\tRatio\tAnova" << endl;
for (int k = 0; k < windows.size(); k++) {
float ds = averageQuery[k] / averageRef[k];
//float fs = varQuery[query] / varRef[query]; /* F-Snedecor, test for differences of variances */
bool results = false;
-
+
//confidence limit, t - Student, anova
out << "Window\tConfidenceLimit\tt-Student\tAnova" << endl;
if (results) {
mothurOut(querySeq->getName() + " was found have at least one chimeric window."); mothurOutEndLine();
}
+
+ //free memory
+ for (int i = 0; i < closest.size(); i++) { delete closest[i].seq; }
+
}
catch(exception& e) {
for (int i = 0; i < closest.size(); i++) { temp.push_back(closest[i].seq); }
temp.push_back(query);
- createFilter(temp);
+ createFilter(temp, 0.5);
for (int i = 0; i < temp.size(); i++) { runFilter(temp[i]); }
determineChimeras(); //fills anova, isChimericConfidence, isChimericTStudent and isChimericANOVA.
- //free memory
- for (int i = 0; i < closest.size(); i++) { delete closest[i].seq; }
-
return 0;
}
catch(exception& e) {
}
sort(topMatches.begin(), topMatches.end(), compareSeqDist);
+
+ for (int i = numWanted; i < topMatches.size(); i++) { delete topMatches[i].seq; }
+
+ topMatches.resize(numWanted);
return topMatches;