X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimoligos.h;h=f3e695406d44a880ed2adc0029e730b6502185fc;hb=7d9e2bc58855132983da7ac9342880bc95055f77;hp=8aa44bdd365356f195069e4f11528300844fbc7a;hpb=10f24e97c62351b0611159a13e116f359deade96;p=mothur.git

diff --git a/trimoligos.h b/trimoligos.h
index 8aa44bd..f3e6954 100644
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -50,10 +50,19 @@ class TrimOligos {
     
         bool stripSpacer(Sequence&);
         bool stripSpacer(Sequence&, QualityScores&);
+    
+        //seq, primerStart, primerEnd
+        bool findForward(Sequence&, int&, int&);
+        bool findReverse(Sequence&, int&, int&);
+    
+        string reverseOligo(string);
+        string getTrashCode() { return trashCode; }
 				
 	
 	private:
 		int pdiffs, bdiffs, ldiffs, sdiffs;
+        bool paired;
+        string trashCode;
 	
 		map<string, int> barcodes;
 		map<string, int> primers;
@@ -72,7 +81,10 @@ 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