added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 54b1d9b4caace40335934db39c6306687ddafdf5..01289a0d0edf66969827d65a11a703c24da86845 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -418,7 +418,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                                
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        abskew = validParameter.validFile(parameters, "abskew", false); if (abskew == "not found"){     useAbskew = false;  abskew = "1.9";     }else{  useAbskew = true;  }
                        if (useAbskew && templatefile != "self") { m->mothurOut("The abskew parameter is only valid with template=self, ignoring."); m->mothurOutEndLine(); useAbskew = false; }
@@ -509,7 +509,7 @@ int ChimeraUchimeCommand::execute(){
                                if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
                                        nameFile = nameFileNames[s];
                                }else { nameFile = getNamesFile(fastaFileNames[s]); }
-                                                                       
+                                                                               
                                map<string, string> seqs;  
                                readFasta(fastaFileNames[s], seqs);  if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {   m->mothurRemove(outputNames[j]);        }  return 0; }
 
@@ -987,6 +987,11 @@ int ChimeraUchimeCommand::driverGroups(SequenceParser& parser, string outputFNam
 
 int ChimeraUchimeCommand::driver(string outputFName, string filename, string accnos, string alns, int& numChimeras){
        try {
+               
+               outputFName = m->getFullPathName(outputFName);
+               filename = m->getFullPathName(filename);
+               alns = m->getFullPathName(alns);
+               
                //to allow for spaces in the path
                outputFName = "\"" + outputFName + "\"";
                filename = "\"" + filename + "\"";