changed random forest output filename

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 882f716357515b008c06889f3f1559a4e4525cd5..53f04d37965d55c189447c7cbd1c702ac93dc5ac 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -299,11 +299,14 @@ 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 +356,13 @@ 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;  }
                     }
@@ -372,11 +375,13 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                         currentSeqsDiffs = thisCurrentSeqsDiffs;
                         barcodeIndex = thisBarcodeIndex;
                         primerIndex = thisPrimerIndex;
-                        currSeq.reverseComplement();
+                        savedSeq.reverseComplement();
+                        currSeq.setAligned(savedSeq.getAligned());
                         if(pDataArray->qFileName != ""){
-                            currQual.flipQScores();
+                            savedQual.flipQScores();
+                            currQual.setScores(savedQual.getScores());
                         }
-                    }
+                    }else { trashCode += "(" + thisTrashCode + ")";  }
                 }