pat's slight modifications to trim.seqs

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 5a0124934bfaeb682914d62aff34a25f04b4a3ab..b430624838594e4185233f7e946733a94469303b 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -322,11 +322,20 @@ int TrimSeqsCommand::execute(){
                                openInputFile(fastaFile, inFASTA);
                                getNumSeqs(inFASTA, numSeqs);
                                inFASTA.close();
-                               qFile.close();
+                               
                                lines.push_back(new linePair(0, numSeqs));
                                
                                driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], lines[0]);
                                
+                               for (int j = 0; j < fastaFileNames.size(); j++) {
+                                       rename((fastaFileNames[j] + toString(j) + ".temp").c_str(), fastaFileNames[j].c_str());
+                               }
+                               if(qFileName != ""){
+                                       for (int j = 0; j < qualFileNames.size(); j++) {
+                                               rename((qualFileNames[j] + toString(j) + ".temp").c_str(), qualFileNames[j].c_str());
+                                       }
+                               }
+                                                                       
                                if (m->control_pressed) {  return 0; }
                #endif
                                                
@@ -479,7 +488,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                        Sequence currSeq(inFASTA);
                        QualityScores currQual;
                        if(qFileName != ""){
-                               currQual = QualityScores(qFile);
+                               currQual = QualityScores(qFile, currSeq.getNumBases());
                        }
                        
                        string origSeq = currSeq.getUnaligned();
@@ -1220,9 +1229,9 @@ int TrimSeqsCommand::countDiffs(string oligo, string seq){
                                else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
                                else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
                                else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
-                               else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }                       
-                               
+                               else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }       
                        }
+                       
                }
                
                return countDiffs;