some changes while testing 1.9

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 919285db14ede39d0afb0a2fff88960869159f50..f565fd301c86126358846076f25e048518c38a10 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -21,7 +21,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","filter","processors","window" "increment","template","conservation","quantile","mask","outputdir","inputdir"};
+                       string Array[] =  {"fasta","filter","processors","window" ,"increment","template","conservation","quantile","mask","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -381,7 +381,7 @@ int ChimeraPintailCommand::execute(){
 
                #else
                        ifstream inFASTA;
-                       openInputFile(candidateFileNames[s], inFASTA);
+                       openInputFile(fastafile, inFASTA);
                        numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
                        inFASTA.close();
                        lines.push_back(new linePair(0, numSeqs));