changed name of parse.fastaq command to fastq.info

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 5fbdfa891db7e57957df05538b5f2f4325684fe4..6912bbb2c79eb03e4a3d899d85369c660e7a0e42 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -187,7 +187,7 @@ CommandFactory::CommandFactory(){
        commands["cluster.fragments"]   = "cluster.fragments";
        commands["get.lineage"]                 = "get.lineage";
        commands["remove.lineage"]              = "remove.lineage";
-       commands["parse.fastaq"]                = "parse.fastaq";
+       commands["fastq.info"]                  = "fastq.info";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -326,7 +326,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "cluster.fragments")             {       command = new ClusterFragmentsCommand(optionString);            }
                else if(commandName == "get.lineage")                   {       command = new GetLineageCommand(optionString);                          }
                else if(commandName == "remove.lineage")                {       command = new RemoveLineageCommand(optionString);                       }
-               else if(commandName == "parse.fastaq")                  {       command = new ParseFastaQCommand(optionString);                         }
+               else if(commandName == "fastq.info")                    {       command = new ParseFastaQCommand(optionString);                         }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;

diff --git a/mothur b/mothur
index ea9c520e0dee3d2f5988c1fc110ff73149bda058..977c74f32988828c64f01fc6e0f1b1dcff4fbf46 100755 (executable)
Binary files a/mothur and b/mothur differ

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 2dece317d758514581ce5e82fc73c16f18afb38f..e808b9b45c7213de48a0f2ceed8a74e59f7e020f 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -19,7 +19,7 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fastaq", "outputdir", "inputdir"};
+                       string Array[] =  {"fastq", "outputdir", "inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -38,18 +38,18 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
                        if (inputDir == "not found"){   inputDir = "";          }
                        else {
                                string path;
-                               it = parameters.find("fastaq");
+                               it = parameters.find("fastq");
                                //user has given a template file
                                if(it != parameters.end()){ 
                                        path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
-                                       if (path == "") {       parameters["fastaq"] = inputDir + it->second;           }
+                                       if (path == "") {       parameters["fastq"] = inputDir + it->second;            }
                                }
                        }
                        
                        //check for required parameters
-                       fastaQFile = validParameter.validFile(parameters, "fastaq", true);
-                       if (fastaQFile == "not found") {        m->mothurOut("fastaq is a required parameter for the parse.fastaq command.");   m->mothurOutEndLine();  abort = true;   }
+                       fastaQFile = validParameter.validFile(parameters, "fastq", true);
+                       if (fastaQFile == "not found") {        m->mothurOut("fastq is a required parameter for the fastq.info command.");      m->mothurOutEndLine();  abort = true;   }
                        else if (fastaQFile == "not open")      {       fastaQFile = ""; abort = true;  }       
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -66,11 +66,11 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
 
 void ParseFastaQCommand::help(){
        try {
-               m->mothurOut("The parse.fastaq command reads a fastaQ file and creates a fasta and quality file.\n");
-               m->mothurOut("The parse.fastaq command parameter is fastaq, and it is required.\n");
-               m->mothurOut("The parse.fastaq command should be in the following format: parse.fastaq(fastaq=yourFastaQFile).\n");
-               m->mothurOut("Example parse.fastaq(fastaq=test.fastaq).\n");
-               m->mothurOut("Note: No spaces between parameter labels (i.e. fastaq), '=' and yourFastaQFile.\n");
+               m->mothurOut("The fastq.info command reads a fastaQ file and creates a fasta and quality file.\n");
+               m->mothurOut("The fastq.info command parameter is fastq, and it is required.\n");
+               m->mothurOut("The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n");
+               m->mothurOut("Example fastq.info(fastaq=test.fastaq).\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n");
                m->mothurOutEndLine();
        }
        catch(exception& e) {