changes while testing

[mothur.git] / makefastqcommand.cpp

diff --git a/makefastqcommand.cpp b/makefastqcommand.cpp
index 995dc6606d86963d64d1bee857233c9656836da6..5a66d9a4b7b23ccd9051803d0e817fc7cf89f315 100644 (file)
--- a/makefastqcommand.cpp
+++ b/makefastqcommand.cpp
@@ -14,10 +14,11 @@
 //**********************************************************************************************************************
 vector<string> MakeFastQCommand::setParameters(){      
        try {
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-               CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pqfile);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fastq",false,true,true); parameters.push_back(pfasta);
+               CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","fastq",false,true,true); parameters.push_back(pqfile);
+               CommandParameter pformat("format", "Multiple", "sanger-illumina-illumina1.8+", "sanger", "", "", "","",false,false); parameters.push_back(pformat);
+        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -32,12 +33,12 @@ vector<string> MakeFastQCommand::setParameters(){
 string MakeFastQCommand::getHelpString(){      
        try {
                string helpString = "";
-               helpString += "The make.fastq command read a fasta and quality file and creates a fastq file.\n";
-               helpString += "The make.fastq command parameters are fasta and qfile, both are required.\n";
-               helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n";
+               helpString += "The make.fastq command reads a fasta and quality file and creates a fastq file.\n";
+               helpString += "The make.fastq command parameters are fasta, qfile and format.  fasta and qfile are required.\n";
+               helpString += "The format parameter is used to indicate whether your sequences are sanger, illumina1.8+ or illumina, default=sanger.\n";
                helpString += "The make.fastq command should be in the following format: make.fastq(qfile=yourQualityFile, fasta=yourFasta).\n";
                helpString += "Example make.fastq(fasta=amazon.fasta, qfile=amazon.qual).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -46,6 +47,21 @@ string MakeFastQCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string MakeFastQCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "fastq") {  pattern = "[filename],fastq"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "MakeFastQCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 MakeFastQCommand::MakeFastQCommand(){  
        try {
                abort = true; calledHelp = true; 
@@ -65,6 +81,7 @@ MakeFastQCommand::MakeFastQCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -115,7 +132,7 @@ MakeFastQCommand::MakeFastQCommand(string option)  {
                                fastafile = m->getFastaFile(); 
                                if (fastafile != "") {  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setFastaFile(fastafile); }   
                        
                        qualfile = validParameter.validFile(parameters, "qfile", true);
                        if (qualfile == "not open") { abort = true; qualfile = ""; }
@@ -123,10 +140,18 @@ MakeFastQCommand::MakeFastQCommand(string option)  {
                                qualfile = m->getQualFile(); 
                                if (qualfile != "") {  m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current qualfile and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setQualFile(qualfile); }     
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);              }
+            
+            format = validParameter.validFile(parameters, "format", false);            if (format == "not found"){     format = "sanger";      }
+            
+            if ((format != "sanger") && (format != "illumina") && (format != "illumina1.8+"))  { 
+                               m->mothurOut(format + " is not a valid format. Your format choices are sanger, illumina1.8+ and illumina, aborting." ); m->mothurOutEndLine();
+                               abort=true;
+                       }
+
 
                }
                
@@ -143,8 +168,9 @@ int MakeFastQCommand::execute(){
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               
-               string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "fastq";
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+               string outputFile = getOutputFileName("fastq",variables);
                outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile);
                
                ofstream out;
@@ -155,7 +181,7 @@ int MakeFastQCommand::execute(){
                
                ifstream fFile;
                m->openInputFile(fastafile, fFile);
-               
+        
                while (!fFile.eof() && !qFile.eof()) {
                        
                        if (m->control_pressed) { break; }
@@ -180,7 +206,7 @@ int MakeFastQCommand::execute(){
                qFile.close();
                out.close();
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -200,9 +226,10 @@ string MakeFastQCommand::convertQual(vector<int> qual) {
        try {
                string qualScores;
                
-               int controlChar = int('!');
-               
-               for (int i = 0; i < qual.size(); i++) { 
+        for (int i = 0; i < qual.size(); i++) { 
+            int controlChar = int('!');
+            if (format == "illumina") {  controlChar = int('@');  }
+            
                        int temp = qual[i] + controlChar;
                        char qualChar = (char) temp;