classify.seqs allows sequences to be in taxonomy file that are not in template. ...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 37c0916d4c49e1f8ed8ca979c7ff61b7e1a13ef3..124fbb876b38def3d61f1bf425ef15f36237fa5f 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1183,7 +1183,7 @@ string MothurOut::sortFile(string distFile, string outputDir){
 
                        string firstName, secondName;
                        float dist;
-                       while (input) {
+                       while (!input.eof()) {
                                input >> firstName >> secondName >> dist;
                                output << dist << '\t' << firstName << '\t' << secondName << endl;
                                gobble(input);
@@ -1199,16 +1199,17 @@ string MothurOut::sortFile(string distFile, string outputDir){
                
                        //read in sorted file and put distance at end again
                        ifstream input2;
+            ofstream output2;
                        openInputFile(tempOutfile, input2);
-                       openOutputFile(outfile, output);
+                       openOutputFile(outfile, output2);
                
-                       while (input2) {
+            while (!input2.eof()) {
                                input2 >> dist >> firstName >> secondName;
-                               output << firstName << '\t' << secondName << '\t' << dist << endl;
+                               output2 << firstName << '\t' << secondName << '\t' << dist << endl;
                                gobble(input2);
                        }
                        input2.close();
-                       output.close();
+                       output2.close();
                
                        //remove temp files
                        mothurRemove(tempDistFile);
@@ -2470,6 +2471,9 @@ void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
 //This function parses the estimator options and puts them in a vector
 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
        try {
+        
+        if (symbol == '-') { splitAtDash(estim, container); return; }
+        
                string individual = "";
                int estimLength = estim.size();
                for(int i=0;i<estimLength;i++){