continued work on chimeras and fixed bug in trim.seqs and reverse.seqs that was due...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 2a982c7135e5b6fc83ed49dbe89cf3804dbc540b..455cdc29aa47ecb1ca26a7f9b4021bef151d6314 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -160,7 +160,7 @@ int TrimSeqsCommand::execute(){
                if(qFileName != "")     {       openInputFile(qFileName, qFile);        }
                
                bool success;
-               
+                       
                while(!inFASTA.eof()){
                        Sequence currSeq(inFASTA);
                        string origSeq = currSeq.getUnaligned();
@@ -173,6 +173,7 @@ int TrimSeqsCommand::execute(){
                                if(!success)                    {       trashCode += 'q';                                                               }
                        }
                        if(barcodes.size() != 0){
+       
                                success = stripBarcode(currSeq, group);
                                if(!success){   trashCode += 'b';       }
                        }
@@ -186,7 +187,8 @@ int TrimSeqsCommand::execute(){
                        }
                        if(minLength > 0 || maxLength > 0){
                                success = cullLength(currSeq);
-                               if(!success){   trashCode += 'l';       }
+                       if ((currSeq.getUnaligned().length() > 300) && (success)) {  cout << "too long " << currSeq.getUnaligned().length() << endl;  }
+                               if(!success){   trashCode += 'l'; }
                        }
                        if(maxHomoP > 0){
                                success = cullHomoP(currSeq);
@@ -200,6 +202,7 @@ int TrimSeqsCommand::execute(){
                        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;