X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimoligos.h;h=5f4f9f06ba48032777e332c3267ae048937d9b48;hb=a89c6295ae9a35fcaaab7fa50dcb68360dd543b0;hp=f3e695406d44a880ed2adc0029e730b6502185fc;hpb=e9845ee4c8db2e044e87d721cc2d94f8d609e03d;p=mothur.git

diff --git a/trimoligos.h b/trimoligos.h
index f3e6954..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 {
 	
@@ -56,13 +48,10 @@ class TrimOligos {
         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;
@@ -85,6 +74,9 @@ class TrimOligos {
         
         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