#include "chimeraccodecommand.h"
#include "ccode.h"
+#include "referencedb.h"
//**********************************************************************************************************************
vector<string> ChimeraCcodeCommand::setParameters(){
try {
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
helpString += "The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n";
helpString += "The window parameter allows you to specify the window size for searching for chimeras. \n";
helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n";
+ helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
helpString += "The chimera.ccode command should be in the following format: \n";
helpString += "chimera.ccode(fasta=yourFastaFile, reference=yourTemplate) \n";
helpString += "Example: chimera.ccode(fasta=AD.align, reference=core_set_aligned.imputed.fasta) \n";
ChimeraCcodeCommand::ChimeraCcodeCommand(string option) {
try {
abort = false; calledHelp = false;
+ ReferenceDB* rdb = ReferenceDB::getInstance();
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
//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 = ""; }
-
- templatefile = validParameter.validFile(parameters, "reference", true);
- if (templatefile == "not open") { abort = true; }
- else if (templatefile == "not found") { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true; }
maskfile = validParameter.validFile(parameters, "mask", false);
if (maskfile == "not found") { maskfile = ""; }
temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "20"; }
convert(temp, numwanted);
+
+ temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
+ save = m->isTrue(temp);
+ rdb->save = save;
+ if (save) { //clear out old references
+ rdb->clearMemory();
+ }
+
+ //this has to go after save so that if the user sets save=t and provides no reference we abort
+ templatefile = validParameter.validFile(parameters, "reference", true);
+ if (templatefile == "not found") {
+ //check for saved reference sequences
+ if (rdb->referenceSeqs.size() != 0) {
+ templatefile = "saved";
+ }else {
+ m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
+ m->mothurOutEndLine();
+ abort = true;
+ }
+ }else if (templatefile == "not open") { abort = true; }
+ else { if (save) { rdb->setSavedReference(templatefile); } }
+
}
}