Pat's fix

[mothur.git] / chimerauchimecommand.h

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index f6e0ab55d5cff328c4a6a247ddb2b72e1ee26df6..b401ae85ae3c22e6d587fd27e649d27db9c6d939 100644 (file)
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -149,6 +149,10 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
        
        try {
                
+               pDataArray->outputFName = pDataArray->m->getFullPathName(pDataArray->outputFName);
+               pDataArray->filename = pDataArray->m->getFullPathName(pDataArray->filename);
+               pDataArray->alns = pDataArray->m->getFullPathName(pDataArray->alns);
+               
                //clears files
                ofstream out, out1, out2;
                pDataArray->m->openOutputFile(pDataArray->outputFName, out); out.close(); 
@@ -326,17 +330,6 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
                                cPara.push_back(tempIdsmoothwindow);
                        }
                        
-                       /*if (useMinsmoothid) {
-                        char* tempminsmoothid = new char[14]; 
-                        //strcpy(tempminsmoothid, "--minsmoothid"); 
-                        *tempminsmoothid = '\0'; strncat(tempminsmoothid, "--minsmoothid", 13);
-                        cPara.push_back(tempminsmoothid);
-                        char* tempMinsmoothid = new char[minsmoothid.length()+1];
-                        *tempMinsmoothid = '\0'; strncat(tempMinsmoothid, minsmoothid.c_str(), minsmoothid.length());
-                        //strcpy(tempMinsmoothid, minsmoothid.c_str());
-                        cPara.push_back(tempMinsmoothid);
-                        }*/
-                       
                        if (pDataArray->useMaxp) {
                                char* tempmaxp = new char[7]; 
                                //strcpy(tempmaxp, "--maxp"); 
@@ -494,6 +487,10 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
        
        try {
                
+               pDataArray->outputFName = pDataArray->m->getFullPathName(pDataArray->outputFName);
+               pDataArray->filename = pDataArray->m->getFullPathName(pDataArray->filename);
+               pDataArray->alns = pDataArray->m->getFullPathName(pDataArray->alns);
+               
                int totalSeqs = 0;
                int numChimeras = 0;