testing 1.13.0

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index eabcc7360bfd8c96793a577b3a98953d33199227..590394670d13ef75ef3ec0e47db7256b18d2e66e 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -231,7 +231,7 @@ int ClearcutCommand::execute() {
                if (jukes)                              {  char* temp = new char[7];  strcpy(temp, "--jukes");  cPara.push_back(temp);          }
                if (kimura)                             { char* temp = new char[8];  strcpy(temp, "--kimura");  cPara.push_back(temp);          }
                if (matrixout != "")    {  
-                       string tempMatrix =  "--matrixout=" + matrixout; 
+                       string tempMatrix =  "--matrixout=" + outputDir + matrixout; 
                        char* temp = new char[tempMatrix.length()];
                        strcpy(temp, tempMatrix.c_str());
                        cPara.push_back(temp);
@@ -262,7 +262,7 @@ int ClearcutCommand::execute() {
                        m->mothurOutEndLine();
                        m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                        m->mothurOut(outputName); m->mothurOutEndLine();
-                       if (matrixout != "")    {  m->mothurOut(matrixout); m->mothurOutEndLine();  }
+                       if (matrixout != "")    {  m->mothurOut(outputDir+matrixout); m->mothurOutEndLine();  }
                        m->mothurOutEndLine();
                }