Fixes windows bug with make.file

source/commands/makefilecommand.cpp

@@ -145,9 +145,7 @@ int MakeFileCommand::execute(){
         
         //find all .fastq files
         string tempFile = inputDir + "fileList.temp";
-        string findCommand = "find \"" + inputDir.substr(0, inputDir.length()-1) + "\" -maxdepth 1 -name \"*." + typeFile + "\"  > \"" + tempFile + "\"";
-        if (m->debug) { m->mothurOut(findCommand + "\n"); }
-        system(findCommand.c_str());
+        fillAccnosFile(tempFile);
         
         //read in list of files
         vector<string> fastqFiles;
@@ -251,4 +249,32 @@ int MakeFileCommand::execute(){
 }
 //**********************************************************************************************************************
 
+int MakeFileCommand::fillAccnosFile(string tempFile){
+    try {
+        
+        string findCommand = "";
+        tempFile = "\"" + tempFile + "\"";
+        
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+        findCommand = "find \"" + inputDir.substr(0, inputDir.length()-1) + "\" -maxdepth 1 -name \"*." + typeFile + " > " + tempFile;
+        if (m->debug) { m->mothurOut(findCommand + "\n"); }
+        system(findCommand.c_str());
+#else
+        //use ls command
+        
+        findCommand = "ls *." + typeFile + " > " + tempFile;
+        if (m->debug) { m->mothurOut(findCommand + "\n"); }
+        system(findCommand.c_str());
+#endif
+        
+        return 0;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "MakeFileCommand", "fillAccnosFile");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
+
 

source/commands/makefilecommand.h

@@ -36,6 +36,8 @@ class MakeFileCommand : public Command {
     vector<string> outputNames;
     int numCols;
     bool abort;
+    
+    int fillAccnosFile(string);
 };