removed various build warnings

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index b098f8f68559c468b48a1fef4dbd34ecc7504db3..e4d0165d136da966addcf3f235a162cad9f5baa1 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -661,7 +661,6 @@ int TrimFlowsCommand::stripBarcode(Sequence& seq, int& group){
                                oligo = oligo.substr(0,alnLength);
                                temp = temp.substr(0,alnLength);
                                
-                               int newStart=0;
                                int numDiff = countDiffs(oligo, temp);
                                
                                if(numDiff < minDiff){
@@ -959,10 +958,8 @@ vector<unsigned long int> TrimFlowsCommand::getFlowFileBreaks() {
                        m->openInputFile(flowFileName, in);
                        in.seekg(spot);
                        
-                       unsigned long int newSpot = spot;
                        string dummy = m->getline(in);
                        
-                       
                        //there was not another sequence before the end of the file
                        unsigned long int sanityPos = in.tellg();