modified seqerror and qualscores

[mothur.git] / parsefastaqcommand.cpp

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index e808b9b45c7213de48a0f2ceed8a74e59f7e020f..7f4fbbab1096101aa8f09931e4c9ac40e04052b1 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -10,12 +10,60 @@
 #include "parsefastaqcommand.h"
 #include "sequence.hpp"
 
+//**********************************************************************************************************************
+vector<string> ParseFastaQCommand::getValidParameters(){       
+       try {
+               string Array[] =  {"fastq", "outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ParseFastaQCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+ParseFastaQCommand::ParseFastaQCommand(){      
+       try {
+               abort = true; calledHelp = true; 
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+               outputTypes["qual"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ParseFastaQCommand::getRequiredParameters(){    
+       try {
+               string Array[] =  {"fastq"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ParseFastaQCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ParseFastaQCommand::getRequiredFiles(){ 
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ParseFastaQCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 ParseFastaQCommand::ParseFastaQCommand(string option){
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
-               if(option == "help") {  help(); abort = true; }
+               if(option == "help") {  help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -33,6 +81,11 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["fasta"] = tempOutNames;
+                       outputTypes["qual"] = tempOutNames;
+                       
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -66,7 +119,7 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
 
 void ParseFastaQCommand::help(){
        try {
-               m->mothurOut("The fastq.info command reads a fastaQ file and creates a fasta and quality file.\n");
+               m->mothurOut("The fastq.info command reads a fastq 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");
@@ -86,14 +139,14 @@ ParseFastaQCommand::~ParseFastaQCommand()  {       /*      do nothing      */      }
 
 int ParseFastaQCommand::execute(){
        try {
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //open Output Files
                string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta";
                string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual";
                ofstream outFasta, outQual;
-               m->openOutputFile(fastaFile, outFasta);  outputNames.push_back(fastaFile);
-               m->openOutputFile(qualFile, outQual);   outputNames.push_back(qualFile);
+               m->openOutputFile(fastaFile, outFasta);  outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile);
+               m->openOutputFile(qualFile, outQual);   outputNames.push_back(qualFile);  outputTypes["qual"].push_back(qualFile);
                
                ifstream in;
                m->openInputFile(fastaQFile, in);
@@ -121,7 +174,7 @@ int ParseFastaQCommand::execute(){
                        if (qual == "") {  m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; break; }
                        
                        //sanity check sequence length and number of quality scores match
-                       if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+                       if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; } }
                        if (qual.length() != sequence.length()) { m->mothurOut("[ERROR]: lengths do not match. read " + toString(sequence.length()) + " characters for fasta and " + toString(qual.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
                        
                        //convert quality scores
@@ -139,7 +192,7 @@ int ParseFastaQCommand::execute(){
                outFasta.close();
                outQual.close();
                
-               if (m->control_pressed) { remove(fastaFile.c_str()); remove(qualFile.c_str()); return 0; }
+               if (m->control_pressed) { outputTypes.clear(); remove(fastaFile.c_str()); remove(qualFile.c_str()); return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();