added order=A or order=B to trim.flows and shhh.flows commands. added load balancing...

[mothur.git] / pcrseqscommand.h

diff --git a/pcrseqscommand.h b/pcrseqscommand.h
index 5ac6437bb730cf03e6e69a8bf7d1562be4aad595..16c1e29be5f9cbba00180a55a746bbe923b3cbdb 100644 (file)
--- a/pcrseqscommand.h
+++ b/pcrseqscommand.h
@@ -77,14 +77,14 @@ struct pcrData {
        unsigned long long fend;
        int count, start, end, length, pdiffs;
        MothurOut* m;
-       vector<string> primers;
+       map<string, int> primers;
     vector<string> revPrimer;
     set<string> badSeqNames;
     bool keepprimer, keepdots;
        
        
        pcrData(){}
-       pcrData(string f, string gf, string bfn, MothurOut* mout, string ol, string ec, vector<string> pr, vector<string> rpr, string nm, bool kp, bool kd, int st, int en, int l, int pd, unsigned long long fst, unsigned long long fen) {
+       pcrData(string f, string gf, string bfn, MothurOut* mout, string ol, string ec, map<string, int> pr, vector<string> rpr, string nm, bool kp, bool kd, int st, int en, int l, int pd, unsigned long long fst, unsigned long long fen) {
                filename = f;
         goodFasta = gf;
         badFasta = bfn;
@@ -132,7 +132,7 @@ static DWORD WINAPI MyPcrThreadFunction(LPVOID lpParam){
         set<int> lengths;
         //pdiffs, bdiffs, primers, barcodes, revPrimers
         map<string, int> faked;
-        TrimOligos trim(pdiffs, 0, primers, faked, revPrimer);
+        TrimOligos trim(pDataArray->pdiffs, 0, pDataArray->primers, faked, pDataArray->revPrimer);
                
                for(int i = 0; i < pDataArray->fend; i++){ //end is the number of sequences to process
             pDataArray->count++;