X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=trimoligos.h;h=5f4f9f06ba48032777e332c3267ae048937d9b48;hb=fefd5ee1517abd3bc38b469cb2dffc85a1571c7e;hp=d72b8146d36bc659ec13ddffc28463ef4a7b8204;hpb=567e4bca5d62bd8ea316ce5def320d070d7507b8;p=mothur.git

diff --git a/trimoligos.h b/trimoligos.h
index d72b814..5f4f9f0 100644
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -15,14 +15,6 @@
 #include "sequence.hpp"
 #include "qualityscores.h"
 
-struct oligosPair {
-	string forward;
-	string reverse;
-	
-	oligosPair() { forward = ""; reverse = "";  }
-	oligosPair(string f, string r) : forward(f), reverse(r) {}
-	~oligosPair() {}
-};
 
 class TrimOligos {
 	
@@ -55,10 +47,11 @@ 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 +70,13 @@ 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);
+        int stripPairedBarcode(Sequence& seq,  int& group);
+        int stripPairedPrimers(Sequence& seq,  int& group);
+
 };
 
 #endif