X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimoligos.h;h=a32b3d8e4f2d388b15b3aa68ed66fa61f33c1681;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=e3ea7d55537e323f3869a6157ff3aed4bbd99eea;hpb=d205e70ae86dbee2efc2df02f2717975854de6ba;p=mothur.git

diff --git a/trimoligos.h b/trimoligos.h
index e3ea7d5..a32b3d8 100644
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -20,11 +20,15 @@ class TrimOligos {
 	
 	public:
         TrimOligos(int,int, map<string, int>, map<string, int>, vector<string>); //pdiffs, bdiffs, primers, barcodes, revPrimers
-		TrimOligos(int,int, int, int, map<string, int>, map<string, int>, vector<string>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimers, linker, spacer
+        TrimOligos(int,int, int, int, map<string, int>, map<string, int>, map<string, int>, vector<string>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimers, linker, spacer
+        TrimOligos(int,int, int, int, map<string, int>, map<string, int>, vector<string>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimers, linker, spacer
 		~TrimOligos();
 	
 		int stripBarcode(Sequence&, int&);	
 		int stripBarcode(Sequence&, QualityScores&, int&);
+    
+        int stripRBarcode(Sequence&, int&);	
+        int stripRBarcode(Sequence&, QualityScores&, int&);
 	
 		int stripForward(Sequence&, int&);
 		int stripForward(Sequence&, QualityScores&, int&, bool);
@@ -43,6 +47,7 @@ class TrimOligos {
 		int pdiffs, bdiffs, ldiffs, sdiffs;
 	
 		map<string, int> barcodes;
+        map<string, int> rbarcodes;
 		map<string, int> primers;
 		vector<string> revPrimer;
         vector<string> linker;