Fixed a bug in the count output of seq.error when using multiple processors

[mothur.git] / trimoligos.h

diff --git a/trimoligos.h b/trimoligos.h
index d72b8146d36bc659ec13ddffc28463ef4a7b8204..f3e695406d44a880ed2adc0029e730b6502185fc 100644 (file)
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -55,10 +55,14 @@ class TrimOligos {
         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;
@@ -77,7 +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