working on pam

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 4d0a6112cb6e288600ae944e9340563f5973da47..14eed17e236a333583d461d61482a1d541c6a9cf 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -55,7 +55,7 @@ private:
        bool abort, createGroup;
        string fastaFile, oligoFile, qFileName, groupfile, nameFile, countfile, outputDir;
        
-       bool flip, allFiles, qtrim, keepforward, pairedOligos, reorient;
+       bool flip, allFiles, qtrim, keepforward, pairedOligos, reorient, logtransform;
        int numFPrimers, numRPrimers, numLinkers, numSpacers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, comboStarts;
        int qWindowSize, qWindowStep, keepFirst, removeLast;
        double qRollAverage, qThreshold, qWindowAverage, qAverage;
@@ -98,7 +98,7 @@ struct trimData {
     vector<vector<string> > qualFileNames;
     vector<vector<string> > nameFileNames;
     unsigned long long lineStart, lineEnd, qlineStart, qlineEnd;
-    bool flip, allFiles, qtrim, keepforward, createGroup, pairedOligos, reorient;
+    bool flip, allFiles, qtrim, keepforward, createGroup, pairedOligos, reorient, logtransform;
        int numFPrimers, numRPrimers, numLinkers, numSpacers, maxAmbig, maxHomoP, minLength, maxLength, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs;
        int qWindowSize, qWindowStep, keepFirst, removeLast, count;
        double qRollAverage, qThreshold, qWindowAverage, qAverage;
@@ -121,7 +121,7 @@ struct 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, vector<string> revP, vector<string> li, vector<string> spa, map<int, oligosPair> pbr, map<int, oligosPair> ppr, bool po,
                       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 WindowStep, int WindowSize, int WindowAverage, bool trim, double Threshold, double Average, double RollAverage, bool lt,
                       int minL, int maxA, int maxH, int maxL, bool fli, bool reo, map<string, string> nm, map<string, int> ncount) {
         filename = fn;
         qFileName = qn;
@@ -174,6 +174,7 @@ struct trimData {
         qThreshold = Threshold;
         qAverage = Average;
         qRollAverage = RollAverage;
+        logtransform = lt;
         minLength = minL;
         maxAmbig = maxA;
         maxHomoP = maxH;
@@ -261,7 +262,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                
         TrimOligos* trimOligos = NULL;
         int numBarcodes = pDataArray->barcodes.size();
-        if (pDataArray->pairedOligos)   {   trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->pairedPrimers, pDataArray->pairedBarcodes);   numBarcodes = pDataArray->pairedBarcodes.size(); }
+        if (pDataArray->pairedOligos)   {   trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->pairedPrimers, pDataArray->pairedBarcodes);   numBarcodes = pDataArray->pairedBarcodes.size(); pDataArray->numFPrimers = pDataArray->pairedPrimers.size(); }
         else                {   trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer);  }
         
         TrimOligos* rtrimOligos = NULL;
@@ -276,6 +277,19 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                 oligosPair tempPair(trimOligos->reverseOligo((it->second).reverse), (trimOligos->reverseOligo((it->second).forward))); //reverseBarcode, rc ForwardBarcode
                 rpairedBarcodes[it->first] = tempPair;
             }
+            
+            int index = rpairedBarcodes.size();
+            for (map<string, int>::iterator it = pDataArray->barcodes.begin(); it != pDataArray->barcodes.end(); it++) {
+                oligosPair tempPair("", trimOligos->reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode
+                rpairedBarcodes[index] = tempPair; index++;
+            }
+            
+            index = rpairedPrimers.size();
+            for (map<string, int>::iterator it = pDataArray->primers.begin(); it != pDataArray->primers.end(); it++) {
+                oligosPair tempPair("", trimOligos->reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode
+                rpairedPrimers[index] = tempPair; index++;
+            }
+
             rtrimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, rpairedPrimers, rpairedBarcodes); numBarcodes = rpairedBarcodes.size();
         }
         
@@ -283,7 +297,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                for(int i = 0; i < pDataArray->lineEnd; i++){ //end is the number of sequences to process
                                   
                        if (pDataArray->m->control_pressed) {
-                delete trimOligos;
+                delete trimOligos; if (pDataArray->reorient) { delete rtrimOligos; }
                                inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
                                if ((pDataArray->createGroup) && (pDataArray->countfile == "")) {        outGroupsFile.close();   }
                 if(pDataArray->qFileName != "")        {       qFile.close();  scrapQualFile.close(); trimQualFile.close();    }
@@ -299,11 +313,14 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                        int currentSeqsDiffs = 0;
             
                        Sequence currSeq(inFASTA); pDataArray->m->gobble(inFASTA);
+            Sequence savedSeq(currSeq.getName(), currSeq.getAligned());
                        
-                       QualityScores currQual;
+                       QualityScores currQual; QualityScores savedQual;
                        if(pDataArray->qFileName != ""){
                                currQual = QualityScores(qFile);  pDataArray->m->gobble(qFile);
+                savedQual.setName(currQual.getName()); savedQual.setScores(currQual.getScores());
                        }
+              
                        
                        string origSeq = currSeq.getUnaligned();
                        if (origSeq != "") {
@@ -353,13 +370,13 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                     int thisPrimerIndex = 0;
                     
                     if(numBarcodes != 0){
-                        thisSuccess = rtrimOligos->stripBarcode(currSeq, currQual, thisBarcodeIndex);
+                        thisSuccess = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex);
                         if(thisSuccess > pDataArray->bdiffs)           {       thisTrashCode += 'b';   }
                         else{ thisCurrentSeqsDiffs += thisSuccess;  }
                     }
                     
                     if(pDataArray->numFPrimers != 0){
-                        thisSuccess = rtrimOligos->stripForward(currSeq, currQual, thisPrimerIndex, pDataArray->keepforward);
+                        thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, pDataArray->keepforward);
                         if(thisSuccess > pDataArray->pdiffs)           {       thisTrashCode += 'f';   }
                         else{ thisCurrentSeqsDiffs += thisSuccess;  }
                     }
@@ -372,7 +389,13 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                         currentSeqsDiffs = thisCurrentSeqsDiffs;
                         barcodeIndex = thisBarcodeIndex;
                         primerIndex = thisPrimerIndex;
-                    }
+                        savedSeq.reverseComplement();
+                        currSeq.setAligned(savedSeq.getAligned());
+                        if(pDataArray->qFileName != ""){
+                            savedQual.flipQScores();
+                            currQual.setScores(savedQual.getScores());
+                        }
+                    }else { trashCode += "(" + thisTrashCode + ")";  }
                 }
 
                 
@@ -407,9 +430,9 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                                        int origLength = currSeq.getNumBases();
                                        
                                        if(pDataArray->qThreshold != 0)                 {       success = currQual.stripQualThreshold(currSeq, pDataArray->qThreshold);                 }
-                                       else if(pDataArray->qAverage != 0)              {       success = currQual.cullQualAverage(currSeq, pDataArray->qAverage);                              }
-                                       else if(pDataArray->qRollAverage != 0)  {       success = currQual.stripQualRollingAverage(currSeq, pDataArray->qRollAverage);  }
-                                       else if(pDataArray->qWindowAverage != 0){       success = currQual.stripQualWindowAverage(currSeq, pDataArray->qWindowStep, pDataArray->qWindowSize, pDataArray->qWindowAverage);       }
+                                       else if(pDataArray->qAverage != 0)              {       success = currQual.cullQualAverage(currSeq, pDataArray->qAverage, pDataArray->logtransform);                            }
+                                       else if(pDataArray->qRollAverage != 0)  {       success = currQual.stripQualRollingAverage(currSeq, pDataArray->qRollAverage, pDataArray->logtransform);        }
+                                       else if(pDataArray->qWindowAverage != 0){       success = currQual.stripQualWindowAverage(currSeq, pDataArray->qWindowStep, pDataArray->qWindowSize, pDataArray->qWindowAverage, pDataArray->logtransform);     }
                                        else                                            {       success = 1;                            }
                                        
                                        //you don't want to trim, if it fails above then scrap it
@@ -567,12 +590,13 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                        }
                        
                        //report progress
-                       if((i) % 1000 == 0){    pDataArray->m->mothurOut(toString(i)); pDataArray->m->mothurOutEndLine();               }
+                       if((pDataArray->count) % 1000 == 0){    pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }
                        
                }
                //report progress
                if((pDataArray->count) % 1000 != 0){    pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }
                
+        if (pDataArray->reorient) { delete rtrimOligos; }
                delete trimOligos;
                inFASTA.close();
                trimFASTAFile.close();