fixed subsample name file name issue. added count parameter to cluster command....

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 9ba64c4b62b7c7e87f213472b730a91bd0b37305..957f37a65bfb1c177f000c9c6d031ddfc3784c81 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -27,6 +27,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "trim.seqs";   }
        string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Trim.seqs"; }
        string getDescription()         { return "provides the preprocessing features needed to screen and sort pyrosequences"; }
@@ -63,6 +64,7 @@ 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 +103,7 @@ 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 +115,7 @@ 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 +144,7 @@ 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 +241,7 @@ 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 +281,13 @@ 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';       }
@@ -404,11 +414,13 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                                                        
                                                        outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
                                                        
+                            int numRedundants = 0;
                                                        if (pDataArray->nameFile != "") {
                                                                map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
                                                                if (itName != pDataArray->nameMap.end()) { 
                                                                        vector<string> thisSeqsNames; 
                                                                        pDataArray->m->splitAtChar(itName->second, thisSeqsNames, ',');
+                                    numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
                                                                        for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
                                                                                outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
                                                                        }
@@ -416,8 +428,8 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                                                        }
                                                        
                                                        map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
-                                                       if (it == pDataArray->groupCounts.end()) {      pDataArray->groupCounts[thisGroup] = 1; }
-                                                       else { pDataArray->groupCounts[it->first]++; }
+                                                       if (it == pDataArray->groupCounts.end()) {      pDataArray->groupCounts[thisGroup] = 1 + numRedundants; }
+                                                       else { pDataArray->groupCounts[it->first] += (1 + numRedundants); }
                             
                                                }
                                        }