added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 9ba64c4b62b7c7e87f213472b730a91bd0b37305..ba4e61411b8498820139e8ae2b1ed71cb37b0432 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -63,6 +63,7 @@ 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;
@@ -101,6 +102,7 @@ struct trimData {
        double qRollAverage, qThreshold, qWindowAverage, qAverage;
     vector<string> revPrimer;
        map<string, int> barcodes;
+    map<string, int> rbarcodes;
        map<string, int> primers;
     vector<string>  linker;
     vector<string>  spacer;
@@ -112,7 +114,7 @@ struct trimData {
     
        trimData(){}
        trimData(string fn, string qn, string nf, string tn, string sn, string tqn, string sqn, string tnn, string snn, 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, 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, map<string, int> rbar, 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) {
@@ -141,6 +143,7 @@ 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();
@@ -237,7 +240,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                }
                
                
-               TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer);
+               TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->rbarcodes, 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
@@ -277,7 +280,13 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                                        if(success > pDataArray->bdiffs)                {       trashCode += 'b';       }
                                        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';       }