version working on mac with .tellg changed to unget for windows

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 1c70a2b5a9723b64a4b9edd34cb2fc81e374e42d..70094f2f3afe77711dcb4fe7b46d70f3d35f4835 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -39,7 +39,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option){
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not found") { cout << "fasta is a required parameter for the screen.seqs command." << endl; abort = true; }
                        else if (fastafile == "not open") { abort = true; }     
-               
+       
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
                        else if (groupfile == "not found") { groupfile = ""; }
@@ -50,7 +50,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option){
 
                        alignreport = validParameter.validFile(parameters, "alignreport", true);
                        if (alignreport == "not open") { abort = true; }
-                       else if (alignreport == "not found") { namefile = ""; } 
+                       else if (alignreport == "not found") { alignreport = ""; }      
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
@@ -160,6 +160,9 @@ int ScreenSeqsCommand::execute(){
                if(groupfile != "")             {       screenGroupFile(badSeqNames);           }
                if(alignreport != "")   {       screenAlignReport(badSeqNames);         }
                
+               goodSeqOut.close();
+               badSeqOut.close();
+               inFASTA.close();
                return 0;
        }
        catch(exception& e) {