added pacbio parameter to fastq.info. fixed issue with paired primers in trim.seqs

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 4b90cda9355112d746999e2a90f9752f5befdf38..935b9a9297e08d1f50e89d4b9a059cf9cbe8e54a 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -686,10 +686,12 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
             for (map<int, oligosPair>::iterator it = pairedPrimers.begin(); it != pairedPrimers.end(); it++) {
                   oligosPair tempPair(reverseOligo((it->second).reverse), (reverseOligo((it->second).forward))); //reversePrimer, rc ForwardPrimer
                 rpairedPrimers[it->first] = tempPair;
+                //cout  << reverseOligo((it->second).reverse) << '\t' << (reverseOligo((it->second).forward)) << '\t' << primerNameVector[it->first] << endl;
             }
             for (map<int, oligosPair>::iterator it = pairedBarcodes.begin(); it != pairedBarcodes.end(); it++) {
                  oligosPair tempPair(reverseOligo((it->second).reverse), (reverseOligo((it->second).forward))); //reverseBarcode, rc ForwardBarcode
                 rpairedBarcodes[it->first] = tempPair;
+                 //cout  << reverseOligo((it->second).reverse) << '\t' << (reverseOligo((it->second).forward)) << '\t' << barcodeNameVector[it->first] << endl;
             }
             rtrimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, rpairedPrimers, rpairedBarcodes); numBarcodes = rpairedBarcodes.size();
         }
@@ -712,13 +714,15 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 
                        Sequence currSeq(inFASTA); m->gobble(inFASTA);
                        //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
+            Sequence savedSeq(currSeq.getName(), currSeq.getAligned());
             
-                       QualityScores currQual;
+                       QualityScores currQual; QualityScores savedQual;
                        if(qFileName != ""){
                                currQual = QualityScores(qFile);  m->gobble(qFile);
+                savedQual.setName(currQual.getName()); savedQual.setScores(currQual.getScores());
                 //cout << currQual.getName() << endl;
                        }
-                       
+                         
                        string origSeq = currSeq.getUnaligned();
                        if (origSeq != "") {
                                
@@ -747,7 +751,11 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                 
                                if(numFPrimers != 0){
                                        success = trimOligos->stripForward(currSeq, currQual, primerIndex, keepforward);
-                                       if(success > pdiffs)            {       trashCode += 'f';       }
+                                       if(success > pdiffs)            {
+                        //if (pairedOligos) {  trashCode += trimOligos->getTrashCode(); }
+                        //else {  trashCode += 'f';  }
+                        trashCode += 'f';
+                    }
                                        else{ currentSeqsDiffs += success;  }
                                }
                                
@@ -767,17 +775,21 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                     int thisPrimerIndex = 0;
                     
                     if(numBarcodes != 0){
-                        thisSuccess = rtrimOligos->stripBarcode(currSeq, currQual, thisBarcodeIndex);
+                        thisSuccess = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex);
                         if(thisSuccess > bdiffs)               {       thisTrashCode += 'b';   }
                         else{ thisCurrentSeqsDiffs += thisSuccess;  }
                     }
                     
                     if(numFPrimers != 0){
-                        thisSuccess = rtrimOligos->stripForward(currSeq, currQual, thisPrimerIndex, keepforward);
-                        if(thisSuccess > pdiffs)               {       thisTrashCode += 'f';   }
+                        thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, keepforward);
+                            if(thisSuccess > pdiffs)           {
+                            //if (pairedOligos) {  thisTrashCode += rtrimOligos->getTrashCode(); }
+                            //else {  thisTrashCode += 'f';  }
+                            thisTrashCode += 'f'; 
+                        }
                         else{ thisCurrentSeqsDiffs += thisSuccess;  }
                     }
-                    
+                   
                     if (thisCurrentSeqsDiffs > tdiffs) {       thisTrashCode += 't';   }
                     
                     if (thisTrashCode == "") { 
@@ -786,9 +798,11 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                         currentSeqsDiffs = thisCurrentSeqsDiffs;
                         barcodeIndex = thisBarcodeIndex;
                         primerIndex = thisPrimerIndex;
-                        currSeq.reverseComplement();
+                        savedSeq.reverseComplement();
+                        currSeq.setAligned(savedSeq.getAligned());
                         if(qFileName != ""){
-                            currQual.flipQScores();
+                            savedQual.flipQScores();
+                            currQual.setScores(savedQual.getScores());
                         }
                     }
                 }
@@ -1551,7 +1565,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {
                                                char c = inOligos.get();
-                                               if (c == 10 || c == 13){        break;  }
+                                               if (c == 10 || c == 13 || c == -1){     break;  }
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        }
@@ -1586,7 +1600,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                     string temp = "";
                     while (!inOligos.eof())    {
                                                char c = inOligos.get();
-                                               if (c == 10 || c == 13){        break;  }
+                                               if (c == 10 || c == 13 || c == -1){     break;  }
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  temp += c;  }
                                        }