added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index f4faacb899a8fd547a14d2bd2224b07882356cdf..414c73cd1d2e6740b89d5200a5c7e7c704097ed6 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -49,7 +49,8 @@ private:
        vector<unsigned long long> getFlowFileBreaks();
        int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
        int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
-
+    string reverseOligo(string);
+    
        vector<string> outputNames;
        set<string> filesToRemove;
        
@@ -66,7 +67,6 @@ private:
        
        string flowFileName, oligoFileName, outputDir;
 
-
        map<string, int> barcodes;
        map<string, int> primers;
        vector<string> revPrimer;