mods to resolve some misc warnings. added alignPrimer function to needle man to allow...

[mothur.git] / trimoligos.h

diff --git a/trimoligos.h b/trimoligos.h
index d72b8146d36bc659ec13ddffc28463ef4a7b8204..df4643c87f1d5b7edd75c5384e7ff2a144a392c7 100644 (file)
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -55,10 +55,12 @@ class TrimOligos {
         bool findForward(Sequence&, int&, int&);
         bool findReverse(Sequence&, int&, int&);
     
+        string reverseOligo(string);
                                
        
        private:
                int pdiffs, bdiffs, ldiffs, sdiffs;
+        bool paired;
        
                map<string, int> barcodes;
                map<string, int> primers;
@@ -77,7 +79,10 @@ class TrimOligos {
                MothurOut* m;
        
                bool compareDNASeq(string, string);                             
-               int countDiffs(string, string);                 
+               int countDiffs(string, string);
+        
+        int stripPairedBarcode(Sequence& seq, QualityScores& qual, int& group);
+        int stripPairedPrimers(Sequence& seq, QualityScores& qual, int& group, bool);
 };
 
 #endif