added dups parameter to chimera.uchime. working on make.contigs command.

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 8d9a57a54ffd0db053956200602f3aa06fb4de5b..1ffad218ccee951e7ac9097d04f84327099fda9d 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -61,7 +61,6 @@ private:
        vector<string> revPrimer, outputNames;
        set<string> filesToRemove;
        map<string, int> barcodes;
-    map<string, int> rbarcodes;
        vector<string> groupVector;
        map<string, int> primers;
     vector<string>  linker;
@@ -102,7 +101,6 @@ struct trimData {
        double qRollAverage, qThreshold, qWindowAverage, qAverage;
     vector<string> revPrimer;
        map<string, int> barcodes;
-    map<string, int> rbarcodes;
        map<string, int> primers;
     map<string, int> nameCount;
     vector<string>  linker;
@@ -116,7 +114,7 @@ struct trimData {
     
        trimData(){}
        trimData(string fn, string qn, string nf, string cf, string tn, string sn, string tqn, string sqn, string tnn, string snn, string tcn, string scn,string gn, vector<vector<string> > ffn, vector<vector<string> > qfn, vector<vector<string> > nfn, unsigned long long lstart, unsigned long long lend, unsigned long long qstart, unsigned long long qend,  MothurOut* mout,
-                      int pd, int bd, int ld, int sd, int td, map<string, int> pri, map<string, int> bar, map<string, int> rbar, vector<string> revP, vector<string> li, vector<string> spa, 
+                      int pd, int bd, int ld, int sd, int td, map<string, int> pri, map<string, int> bar, vector<string> revP, vector<string> li, vector<string> spa, 
                       vector<string> priNameVector, vector<string> barNameVector, bool cGroup, bool aFiles, bool keepF, int keepfi, int removeL,
                       int WindowStep, int WindowSize, int WindowAverage, bool trim, double Threshold, double Average, double RollAverage,
                       int minL, int maxA, int maxH, int maxL, bool fli, map<string, string> nm, map<string, int> ncount) {
@@ -149,7 +147,6 @@ struct trimData {
         sdiffs = sd;
         tdiffs = td;
         barcodes = bar;
-        rbarcodes = rbar;
         primers = pri;      numFPrimers = primers.size();
         revPrimer = revP;   numRPrimers = revPrimer.size();
         linker = li;        numLinkers = linker.size();
@@ -254,7 +251,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                }
                
                
-               TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->rbarcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer);
+               TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer);
         
                pDataArray->count = pDataArray->lineEnd;
                for(int i = 0; i < pDataArray->lineEnd; i++){ //end is the number of sequences to process
@@ -299,12 +296,6 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                                        else{ currentSeqsDiffs += success;  }
                                }
                 
-                               if(pDataArray->rbarcodes.size() != 0){
-                                       success = trimOligos.stripRBarcode(currSeq, currQual, barcodeIndex);
-                                       if(success > pDataArray->bdiffs)                {       trashCode += 'b';       }
-                                       else{ currentSeqsDiffs += success;  }
-                               }
-                
                 if(pDataArray->numSpacers != 0){
                                        success = trimOligos.stripSpacer(currSeq, currQual);
                                        if(success > pDataArray->sdiffs)                {       trashCode += 's';       }