added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index 46da9137a18c072bfc1033025fd2551ea92c728a..63a90148699985581c80febe11288a99d5cd87bf 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -80,15 +80,9 @@ void Pintail::doPrep() {
                bool reRead = false;
                //create filter if needed for later
                if (filter) {
-                       reRead = true;
-                       
-                       if (seqMask != "") {
-                               //mask templates
-                               for (int i = 0; i < templateSeqs.size(); i++) {
-                                       decalc->runMask(templateSeqs[i]);
-                               }
-                       }
                        
+cout << "filter" << endl;                      
+                                               
                        //read in all query seqs
                        ifstream in; 
                        openInputFile(fastafile, in);
@@ -106,11 +100,20 @@ void Pintail::doPrep() {
                        //merge query seqs and template seqs
                        temp = templateSeqs;
                        for (int i = 0; i < tempQuerySeqs.size(); i++) {  temp.push_back(tempQuerySeqs[i]);  }
-                       
+cout << temp.size() << endl;   
+                       if (seqMask != "") {
+                           reRead = true;
+       cout << "masked "  << seqMask << endl;
+                               //mask templates
+                               for (int i = 0; i < temp.size(); i++) {
+                                       decalc->runMask(temp[i]);
+                               }
+                       }
+
                        mergedFilterString = createFilter(temp, 0.5);
-                       
+       cout << "here" << endl;         
                        //reread template seqs
-                       for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
+                       //for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
                }
                
                
@@ -128,6 +131,13 @@ void Pintail::doPrep() {
                                }
                        }
                        
+                       if (filter) { 
+                               reRead = true;
+                               for (int i = 0; i < templateSeqs.size(); i++) {
+                                       runFilter(templateSeqs[i]);
+                               }
+                       }
+                       
                        mothurOut("Calculating quantiles for your template.  This can take a while...  I will output the quantiles to a .quan file that you can input them using the quantiles parameter next time you run this command.  Providing the .quan file will dramatically improve speed.    "); cout.flush();
                        if (processors == 1) { 
                                quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
@@ -139,19 +149,20 @@ void Pintail::doPrep() {
                        
                        if ((!filter) && (seqMask == "")) {
                                noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.quan";
-                       }else if ((filter) && (seqMask == "")) { 
-                               noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered.quan";
                        }else if ((!filter) && (seqMask != "")) { 
                                noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.masked.quan";
                        }else if ((filter) && (seqMask != "")) { 
-                               noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered.masked.quan";
+                               noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered." + getSimpleName(getRootName(fastafile)) + "masked.quan";
+                       }else if ((filter) && (seqMask == "")) { 
+                               noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered." + getSimpleName(getRootName(fastafile)) + "quan";
                        }
 
+
+
                                                
                        decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());
                        
-                       openOutputFile(noOutliers, out5);
-                       
+                       openOutputFile(noOutliers, out5);                       
                        //adjust quantiles
                        for (int i = 0; i < quantilesMembers.size(); i++) {
                                vector<float> temp;
@@ -209,7 +220,7 @@ void Pintail::doPrep() {
        }
 }
 //***************************************************************************************************************
-void Pintail::print(ostream& out) {
+void Pintail::print(ostream& out, ostream& outAcc) {
        try {
                int index = ceil(deviation);
                
@@ -227,6 +238,7 @@ void Pintail::print(ostream& out) {
                out << querySeq->getName() << '\t' << "div: " << deviation << "\tstDev: " << DE << "\tchimera flag: " << chimera << endl;
                if (chimera == "Yes") {
                        mothurOut(querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera); mothurOutEndLine();
+                       outAcc << querySeq->getName() << endl;
                }
                out << "Observed\t";