added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / trimoligos.h

diff --git a/trimoligos.h b/trimoligos.h
index e3ea7d55537e323f3869a6157ff3aed4bbd99eea..a32b3d8e4f2d388b15b3aa68ed66fa61f33c1681 100644 (file)
--- 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;