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 f6e0ab55d5cff328c4a6a247ddb2b72e1ee26df6..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(); 
@@ -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;