fixed some bugs found while testing 1.8

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 4dc07a7afa207f80b026077b7abfbbb27bb498c2..70b1b4ae8a0c931ff3f84a56d4dd68fa1edd537a 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -105,7 +105,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option){
                        
                        temp = validParameter.validFile(parameters, "qfile", true);     
                        if (temp == "not found")        {       qFileName = "";         }
-                       else if(temp == "not open")     {       abort = 0;              }
+                       else if(temp == "not open")     {       abort = true;           }
                        else                                            {       qFileName = temp;       }
                        
                        temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
@@ -183,7 +183,10 @@ int TrimSeqsCommand::execute(){
        try{
        
                if (abort == true) { return 0; }
-
+               
+               numFPrimers = 0;  //this needs to be initialized
+               numRPrimers = 0;
+               
                ifstream inFASTA;
                openInputFile(fastaFile, inFASTA);
                
@@ -207,9 +210,10 @@ int TrimSeqsCommand::execute(){
                if(qFileName != "")     {       openInputFile(qFileName, qFile);        }
                
                bool success;
-                       
+
                while(!inFASTA.eof()){
                        Sequence currSeq(inFASTA);
+
                        string origSeq = currSeq.getUnaligned();
                        if (origSeq != "") {
                                int group;
@@ -223,21 +227,22 @@ int TrimSeqsCommand::execute(){
                                        }
                                        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(!success){   trashCode += 'l'; }
@@ -299,8 +304,7 @@ int TrimSeqsCommand::execute(){
                        outGroups.close();
                        inFASTA.close();
                }
-               
-               
+                       
                return 0;               
        }
        catch(exception& e) {