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

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 0846bbd9d1755f73e690e4bf11f72f0282fdfe25..40b3f2683fbdc47770dd3a4292df5ae8cc6fbf75 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -987,6 +987,11 @@ int ChimeraUchimeCommand::driverGroups(SequenceParser& parser, string outputFNam
 
 int ChimeraUchimeCommand::driver(string outputFName, string filename, string accnos, string alns, int& numChimeras){
        try {
+               
+               outputFName = m->getFullPathName(outputFName);
+               filename = m->getFullPathName(filename);
+               alns = m->getFullPathName(alns);
+               
                //to allow for spaces in the path
                outputFName = "\"" + outputFName + "\"";
                filename = "\"" + filename + "\"";