paralellized seq.error and dist.shared added some error checks to libshuff and dist...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 64522a5f157820e529b3261d0acaf898f32136b6..dc87fff99489ebe9ebfc29bec6ff2328875d7030 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -240,7 +240,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "name", true);      
                        if (temp == "not found")        {       nameFile = "";          }
-                       else if(temp == "not open")     {       abort = true;           }
+                       else if(temp == "not open")     {       nameFile = "";  abort = true;           }
                        else                                            {       nameFile = temp;        }
                        
                        temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
@@ -818,10 +818,14 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                ofstream temp;
                m->openOutputFile(trimFASTAFileName, temp);             temp.close();
                m->openOutputFile(scrapFASTAFileName, temp);    temp.close();
-               m->openOutputFile(trimQualFileName, temp);              temp.close();
-               m->openOutputFile(scrapQualFileName, temp);             temp.close();
-               m->openOutputFile(trimNameFileName, temp);              temp.close();
-               m->openOutputFile(scrapNameFileName, temp);             temp.close();
+               if(qFileName != ""){
+                       m->openOutputFile(trimQualFileName, temp);              temp.close();
+                       m->openOutputFile(scrapQualFileName, temp);             temp.close();
+               }
+               if (nameFile != "") {
+                       m->openOutputFile(trimNameFileName, temp);              temp.close();
+                       m->openOutputFile(scrapNameFileName, temp);             temp.close();
+               }
 
                driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, trimNameFileName, scrapNameFileName, groupFile, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);