X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimoligos.h;h=a86eb9ae1c815a8c71c4331934f88bf6b83f773f;hp=6716deb464eb0198b00159490d1f33572c6c6d23;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=a9dbc22713bfc056a797361dd757b1a5c98e1c01

diff --git a/trimoligos.h b/trimoligos.h
index 6716deb..a86eb9a 100644
--- 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 +50,16 @@ 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);
 	
 	private:
 		int pdiffs, bdiffs, ldiffs, sdiffs;
+        bool paired;
 	
 		map<string, int> barcodes;
 		map<string, int> primers;
@@ -70,7 +78,10 @@ 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