openOutputFile(freqfile, outFreq);
+ outFreq << "#" << m->getVersion() << endl;
+
string length = toString(seqs.size()); //if there are 5000 seqs in the template then set precision to 3
int precision = length.length() - 1;
}
//***************************************************************************************************************
//seqs have already been masked
-vector< vector<quanMember> > DeCalculator::getQuantiles(vector<Sequence*> seqs, vector<int> windowSizesTemplate, int window, vector<float> probProfile, int increment, int start, int end) {
+vector< vector<float> > DeCalculator::getQuantiles(vector<Sequence*> seqs, vector<int> windowSizesTemplate, int window, vector<float> probProfile, int increment, int start, int end) {
try {
- vector< vector<quanMember> > quan;
+ vector< vector<float> > quan;
//percentage of mismatched pairs 1 to 100
quan.resize(100);
//cout << i << '\t' << j << '\t' << dist << '\t' << de << endl;
dist = ceil(dist);
- quanMember newScore(de, i, j);
+ //quanMember newScore(de, i, j);
- quan[dist].push_back(newScore);
+ quan[dist].push_back(de);
delete subject;
}
}
//***************************************************************************************************************
//this was going to be used by pintail to increase the sensitivity of the chimera detection, but it wasn't quite right. may want to revisit in the future...
-void DeCalculator::removeObviousOutliers(vector< vector<quanMember> >& quantiles, int num) {
+void DeCalculator::removeObviousOutliers(vector< vector<float> >& quantiles, int num) {
try {
for (int i = 0; i < quantiles.size(); i++) {
//find mean of this quantile score
- sort(quantiles[i].begin(), quantiles[i].end(), compareQuanMembers);
+ sort(quantiles[i].begin(), quantiles[i].end());
- vector<quanMember> temp;
+ vector<float> temp;
if (quantiles[i].size() != 0) {
- float high = quantiles[i][int(quantiles[i].size() * 0.99)].score;
- float low = quantiles[i][int(quantiles[i].size() * 0.01)].score;
+ float high = quantiles[i][int(quantiles[i].size() * 0.99)];
+ float low = quantiles[i][int(quantiles[i].size() * 0.01)];
//look at each value in quantiles to see if it is an outlier
for (int j = 0; j < quantiles[i].size(); j++) {
//is this score between 1 and 99%
- if ((quantiles[i][j].score > low) && (quantiles[i][j].score < high)) {
+ if ((quantiles[i][j] > low) && (quantiles[i][j] < high)) {
temp.push_back(quantiles[i][j]);
}
}