fixed some bugs found while testing 1.8

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index efc45c191482cc191fa204e526758a81af4bf910..1fe2300387a96e81500a0b41c76190df02aba935 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -65,7 +65,7 @@ int SharedCommand::execute(){
                //lookup.clear();
                string errorOff = "no error";
                //errorOff = "";
-cout << globaldata->inputFileName << endl;                     
+               
                //read in listfile
                read = new ReadOTUFile(globaldata->inputFileName);      
                read->read(&*globaldata); 
@@ -101,7 +101,7 @@ cout << globaldata->inputFileName << endl;
                                groups += globaldata->Groups[i] + ".";
                        }
                
-                       string newGroupFile = getRootName(globaldata->inputFileName) + groups + "groups";
+                       string newGroupFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + groups + "groups";
                        ofstream outGroups;
                        openOutputFile(newGroupFile, outGroups);
                
@@ -199,7 +199,13 @@ cout << globaldata->inputFileName << endl;
                        delete it3->second;
                }
 
+               
+               //change format to shared  to speed up commands
+               globaldata->setFormat("sharedfile");
+               globaldata->setListFile("");
+               globaldata->setGroupFile("");
                globaldata->setSharedFile(filename);
+
                
                return 0;
        }
@@ -274,7 +280,7 @@ void SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
 void SharedCommand::createMisMatchFile() {
        try {
                ofstream outMisMatch;
-               string outputMisMatchName = getRootName(globaldata->inputFileName);
+               string outputMisMatchName = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
                
                //you have sequences in your list file that are not in your group file
                if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {