X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=b5357b38e1e3bf892ef7f0cd9ffcfb7b7de4ec8a;hb=a86aff4f80701bf0d436f02c0095920114e1cba2;hp=a4a4215277fadbdb5857dea6d9e9319e233cad01;hpb=a8367302932de9be5434e77f6e5829d7609e2aec;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index a4a4215..b5357b3 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -33,7 +33,7 @@ private:
 	bool stripQualThreshold(Sequence&, ifstream&);
 	bool cullQualAverage(Sequence&, ifstream&);
 	int stripBarcode(Sequence&, int&);
-	int stripForward(Sequence&);
+	int stripForward(Sequence&, int&);
 	bool stripReverse(Sequence&);
 	bool cullLength(Sequence&);
 	bool cullHomoP(Sequence&);
@@ -45,10 +45,12 @@ private:
 	string fastaFile, oligoFile, qFileName, outputDir;
 	
 	bool flip, allFiles, qtrim;
-	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs;
-	vector<string> forPrimer, revPrimer, outputNames;
+	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs, comboStarts;
+	vector<string> revPrimer, outputNames;
 	map<string, int> barcodes;
 	vector<string> groupVector;
+	map<string, int> primers;
+	map<string, int> combos;
 	
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;