added qvalues to metastats. fixed bug with chimera.uchime location. fixed windows...

[mothur.git] / chimerauchimecommand.h

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 6e1f809ce55a332020240bdc0b5e30398b5d5b49..45dd8a8ef332f634564c3911b18b96ae641a49dc 100644 (file)
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -149,6 +149,10 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
        
        try {
                
+               pDataArray->outputFName = pDataArray->m->getFullPathName(outputFName);
+               pDataArray->filename = pDataArray->m->getFullPathName(filename);
+               pDataArray->alns = pDataArray->m->getFullPathName(alns);
+               
                //clears files
                ofstream out, out1, out2;
                pDataArray->m->openOutputFile(pDataArray->outputFName, out); out.close(); 
@@ -181,7 +185,7 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
                        
                        string path = pDataArray->m->argv;
                        string tempPath = path;
-                       for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+                       for (int j = 0; j < path.length(); j++) { tempPath[j] = tolower(path[j]); }
                        path = path.substr(0, (tempPath.find_last_of('m')));
                        
                        string uchimeCommand = path;
@@ -494,6 +498,10 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
        
        try {
                
+               pDataArray->outputFName = pDataArray->m->getFullPathName(outputFName);
+               pDataArray->filename = pDataArray->m->getFullPathName(filename);
+               pDataArray->alns = pDataArray->m->getFullPathName(alns);
+               
                int totalSeqs = 0;
                int numChimeras = 0;