added linker and spacer to trim.flows

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 0dc1cd977c9b106b4986e2cb839939cae7541db2..8c996dd9782734a5e9e209ecea4a57f1b1e1d333 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -58,7 +58,7 @@ private:
        bool allFiles;
        int processors;
        int numFPrimers, numRPrimers;
-       int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+       int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
        int numFlows;
        float signal, noise;
        bool fasta;
@@ -70,6 +70,8 @@ private:
        map<string, int> barcodes;
        map<string, int> primers;
        vector<string> revPrimer;
+    vector<string> linker;
+    vector<string> spacer;
 
        vector<string> primerNameVector;        //needed here?
        vector<string> barcodeNameVector;       //needed here?