modified sequence class to read fasta files with comments. this required modification...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 5ca70a99cb4b600780b425ff7f29b909794cc362..ca7a927134f1f904401ab017d456ff1f6859a569 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -173,61 +173,63 @@ int TrimSeqsCommand::execute(){
                while(!inFASTA.eof()){
                        Sequence currSeq(inFASTA);
                        string origSeq = currSeq.getUnaligned();
-                       int group;
-                       string trashCode = "";
-                       
-                       if(qFileName != ""){
-                               if(qThreshold != 0)             {       success = stripQualThreshold(currSeq, qFile);   }
-                               else if(qAverage != 0)  {       success = cullQualAverage(currSeq, qFile);              }
-                               if ((!qtrim) && (origSeq.length() != currSeq.getUnaligned().length())) { 
-                                       success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
+                       if (origSeq != "") {
+                               int group;
+                               string trashCode = "";
+                               
+                               if(qFileName != ""){
+                                       if(qThreshold != 0)             {       success = stripQualThreshold(currSeq, qFile);   }
+                                       else if(qAverage != 0)  {       success = cullQualAverage(currSeq, qFile);              }
+                                       if ((!qtrim) && (origSeq.length() != currSeq.getUnaligned().length())) { 
+                                               success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
+                                       }
+                                       if(!success)                    {       trashCode += 'q';                                                               }
                                }
-                               if(!success)                    {       trashCode += 'q';                                                               }
-                       }
-                       if(barcodes.size() != 0){
-       
-                               success = stripBarcode(currSeq, group);
-                               if(!success){   trashCode += 'b';       }
-                       }
-                       if(numFPrimers != 0){
-                               success = stripForward(currSeq);
-                               if(!success){   trashCode += 'f';       }
-                       }
-                       if(numRPrimers != 0){
-                               success = stripReverse(currSeq);
-                               if(!success){   trashCode += 'r';       }
-                       }
-                       if(minLength > 0 || maxLength > 0){
-                               success = cullLength(currSeq);
-                       if ((currSeq.getUnaligned().length() > 300) && (success)) {  cout << "too long " << currSeq.getUnaligned().length() << endl;  }
-                               if(!success){   trashCode += 'l'; }
-                       }
-                       if(maxHomoP > 0){
-                               success = cullHomoP(currSeq);
-                               if(!success){   trashCode += 'h';       }
-                       }
-                       if(maxAmbig != -1){
-                               success = cullAmbigs(currSeq);
-                               if(!success){   trashCode += 'n';       }
-                       }
-                       
-                       if(flip){       currSeq.reverseComplement();    }               // should go last                       
-                       
-                       if(trashCode.length() == 0){
-                               currSeq.setAligned(currSeq.getUnaligned());  //this is because of a modification we made to the sequence class to fix a bug.  all seqs have an aligned version, which is the version that gets printed.
-                               currSeq.printSequence(outFASTA);
                                if(barcodes.size() != 0){
-                                       outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
                                        
-                                       if(allFiles){
-                                               currSeq.printSequence(*fastaFileNames[group]);                                  
+                                       success = stripBarcode(currSeq, group);
+                                       if(!success){   trashCode += 'b';       }
+                               }
+                               if(numFPrimers != 0){
+                                       success = stripForward(currSeq);
+                                       if(!success){   trashCode += 'f';       }
+                               }
+                               if(numRPrimers != 0){
+                                       success = stripReverse(currSeq);
+                                       if(!success){   trashCode += 'r';       }
+                               }
+                               if(minLength > 0 || maxLength > 0){
+                                       success = cullLength(currSeq);
+                                       if ((currSeq.getUnaligned().length() > 300) && (success)) {  cout << "too long " << currSeq.getUnaligned().length() << endl;  }
+                                       if(!success){   trashCode += 'l'; }
+                               }
+                               if(maxHomoP > 0){
+                                       success = cullHomoP(currSeq);
+                                       if(!success){   trashCode += 'h';       }
+                               }
+                               if(maxAmbig != -1){
+                                       success = cullAmbigs(currSeq);
+                                       if(!success){   trashCode += 'n';       }
+                               }
+                               
+                               if(flip){       currSeq.reverseComplement();    }               // should go last                       
+                               
+                               if(trashCode.length() == 0){
+                                       currSeq.setAligned(currSeq.getUnaligned());  //this is because of a modification we made to the sequence class to fix a bug.  all seqs have an aligned version, which is the version that gets printed.
+                                       currSeq.printSequence(outFASTA);
+                                       if(barcodes.size() != 0){
+                                               outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
+                                               
+                                               if(allFiles){
+                                                       currSeq.printSequence(*fastaFileNames[group]);                                  
+                                               }
                                        }
                                }
-                       }
-                       else{
-                               currSeq.setName(currSeq.getName() + '|' + trashCode);
-                               currSeq.setUnaligned(origSeq);
-                               currSeq.printSequence(scrapFASTA);
+                               else{
+                                       currSeq.setName(currSeq.getName() + '|' + trashCode);
+                                       currSeq.setUnaligned(origSeq);
+                                       currSeq.printSequence(scrapFASTA);
+                               }
                        }
                        gobble(inFASTA);
                }