X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimoligos.h;h=a86eb9ae1c815a8c71c4331934f88bf6b83f773f;hp=d72b8146d36bc659ec13ddffc28463ef4a7b8204;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=7f1aca4ed9e6db70de82e80ca4771f7680b21d26

diff --git a/trimoligos.h b/trimoligos.h
index d72b814..a86eb9a 100644
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -55,10 +55,11 @@ 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 +78,10 @@ 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