X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.cpp;h=e4d0165d136da966addcf3f235a162cad9f5baa1;hb=e6c4a7223199d800d496356604eb34dfe273673d;hp=b098f8f68559c468b48a1fef4dbd34ecc7504db3;hpb=73fb1fe84d565ea9a0ff793de990546b177310c8;p=mothur.git

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index b098f8f..e4d0165 100644
--- 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();