Merge remote-tracking branch 'mothur/master'

[mothur.git] / trimoligos.h

diff --git a/trimoligos.h b/trimoligos.h
index 6716deb464eb0198b00159490d1f33572c6c6d23..f3e695406d44a880ed2adc0029e730b6502185fc 100644 (file)
--- a/trimoligos.h
+++ b/trimoligos.h
@@ -35,10 +35,12 @@ class TrimOligos {
                int stripBarcode(Sequence&, int&);      
                int stripBarcode(Sequence&, QualityScores&, int&);
         int stripBarcode(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
+        int stripBarcode(Sequence&, Sequence&, int&);
        
                int stripForward(Sequence&, int&);
                int stripForward(Sequence&, QualityScores&, int&, bool);
         int stripForward(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
+        int stripForward(Sequence&, Sequence&, int&);
        
                bool stripReverse(Sequence&);
                bool stripReverse(Sequence&, QualityScores&);
@@ -48,10 +50,19 @@ class TrimOligos {
     
         bool stripSpacer(Sequence&);
         bool stripSpacer(Sequence&, QualityScores&);
+    
+        //seq, primerStart, primerEnd
+        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;
@@ -70,7 +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