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Settings.cpp
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Settings.cpp
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/*******************************************************************************
* Copyright (C) 2014, 2015 Giles Miclotte (giles.miclotte@intec.ugent.be) *
* This file is part of Jabba *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
*******************************************************************************/
#include "Settings.hpp"
#include <cstdlib>
#include <iostream>
#include <cstdio>
#include <fstream>
#include <cassert>
#include <sstream>
#include <algorithm>
#include <cmath>
#include <thread>
Settings::Settings(int argc, char** args)
{
// parse program arguments
if (argc < 4) {
if (argc == 1) {
printProgramInfo();
} else {
std::string arg = args[1];
if (arg == "-h" || arg == "--help") {
printUsage();
exit(EXIT_SUCCESS);
} else if (arg == "-i" || arg == "--info") {
printProgramInfo();
exit(EXIT_SUCCESS);
}
}
printUsage();
exit(EXIT_FAILURE);
}
//set standard values
num_threads_ = std::thread::hardware_concurrency();
essa_k_ = 1;
max_passes_ = 2;
min_len_ = 20;
directory_ = "Jabba_output";
output_mode_ = SHORT;
std::string graph_name = "DBGraph.fasta";
FileType file_type(FASTA);
std::vector<std::string> libraries;
// extract the other parameters
for (int i = 1; i < argc; i++) {
std::string arg(args[i]);
if (arg.empty()) continue;// this shouldn't happen
if (arg == "-fastq") { // file type
std::cout << "FileType is fastq." << std::endl;
file_type = FASTQ;
} else if (arg == "-fasta") {
std::cout << "FileType is fasta." << std::endl;
file_type = FASTA;
} else if (arg == "-t" || arg == "--threads") {
++i;
num_threads_ = std::stoi(args[i]);
} else if (arg == "-g" || arg == "--graph") {
++i;
graph_name = args[i];
} else if (arg == "-k" || arg == "--dbgk") {
++i;
dbg_k_ = std::stoi(args[i]);
} else if (arg == "-e" || arg == "--essak") {
++i;
essa_k_ = std::stoi(args[i]);
} else if (arg == "-p" || arg == "--passes") {
++i;
max_passes_ = std::stoi(args[i]);
} else if (arg == "-l" || arg == "--length") {
++i;
min_len_ = std::stoi(args[i]);
} else if (arg == "-o" || arg == "--output") {
++i;
directory_ = args[i];
} else if (arg == "-s" || arg == "--short") {
std::cerr << "-s --short is deprecated, short is now the default output mode.\n";
output_mode_ = SHORT;
} else if (arg == "-m" || arg == "--outputmode") {
++i;
if (std::string(args[i]) == std::string("short")) {
output_mode_ = SHORT;
} else if (std::string(args[i]) == std::string("long")) {
output_mode_ = LONG;
} else {
std::cerr << args[i] << " is not a valid output mode. Use \"long\" or \"short\" instead.\n";
}
} else {// filename
libraries.push_back(args[i]);
}
}
for (auto const &lib : libraries) {
libraries_.insert(ReadLibrary(lib, directory_));
}
//
graph_ = new ReadLibrary(graph_name, "");
// try to create the output directory
#ifdef _MSC_VER
CreateDirectory(directory_.c_str(), NULL);
#else
DIR * dir = opendir(directory_.c_str());
if ((dir == NULL) && (mkdir(directory_.c_str(), 0777) != 0))
throw std::ios_base::failure("Can't create directory: " + directory_);
closedir(dir);
#endif
// log the instructions
logInstructions(argc, args);
//print settings
std::cout << "Max Number of Threads is " << num_threads_ << std::endl;
std::cout << "Graph is " << graph_->getInputFilename() << std::endl;
std::cout << "DBG K is " << dbg_k_ << std::endl;
std::cout << "ESSA K is " << essa_k_ << std::endl;
std::cout << "Max Passes is " << max_passes_ << std::endl;
std::cout << "Min Seed Size is " << min_len_ << std::endl;
std::cout << "Output Directory is " << directory_ << std::endl;
std::cout << "Output Mode is ";
if (output_mode_ == SHORT){
std::cout << "short" << std::endl;
} else if (output_mode_ == LONG){
std::cout << "long" << std::endl;
} else {
std::cout << "not implemented" << std::endl;
}
}
void Settings::printProgramInfo() const {
std::cout << "Jabba: Hybrid Error Correction." << std::endl;
std::cout << "Jabba v." << JABBA_MAJOR_VERSION << "."
<< JABBA_MINOR_VERSION << "." << JABBA_PATCH_LEVEL << "\n";
std::cout << "Copyright 2014, 2015 Giles Miclotte (giles.miclotte@intec.ugent.be)\n";
std::cout << "This is free software; see the source for copying conditions. "
"There is NO\nwarranty; not even for MERCHANTABILITY or "
"FITNESS FOR A PARTICULAR PURPOSE.\n" << std::endl;
std::cout << std::endl;
}
void Settings::printUsage() const {
std::cout << "Usage: Jabba [options] [file_options] file1 [[file_options] file2]...\n";
std::cout << "Corrects sequence reads in file(s)\n\n";
std::cout << " [options]\n";
std::cout << " -h\t--help\t\tdisplay help page\n";
std::cout << " -i\t--info\t\tdisplay information page\n";
std::cout << " [options arg]\n";
std::cout << " -l\t--length\tminimal seed size [default = 20]\n";
std::cout << " -k\t--dbgk\t\tde Bruijn graph k-mer size\n";
std::cout << " -e\t--essak\t\tsparseness factor of the enhance suffix array [default = 1]\n";
std::cout << " -t\t--threads\tnumber of threads [default = available cores]\n";
std::cout << " -p\t--passes\tmaximal number of passes per read [default = 2]\n";
std::cout << " -m\t--outputmode\tshort (do not extend the reads) or long (maximally extend reads) [default = short]\n";
std::cout << " [file_options file_name]\n";
std::cout << " -o\t--output\toutput directory [default = Jabba_output]\n";
std::cout << " -fastq\t\tfastq input files\n";
std::cout << " -fasta\t\tfasta input files\n";
std::cout << " -g\t--graph\t\tgraph input file [default = DBGraph.fasta]\n\n";
std::cout << " examples:\n";
std::cout << " ./Jabba --dbgk 31 --graph DBGraph.txt -fastq reads.fastq\n";
std::cout << " ./Jabba -o Jabba -l 20 -k 31 -p 2 -e 12 -g DBGraph.txt -fastq reads.fastq\n";
}
std::string Settings::getLogFilename() const {
return directory_ + "/log";
}
void Settings::logInstructions(int argc, char **args) const {
std::ofstream logFile;
logFile.open(getLogFilename().c_str());
if (!logFile)
throw std::ios_base::failure("Can't write to " + getLogFilename());
for (int i = 0; i < argc; i++)
logFile << " " << args[i];
logFile << std::endl;
logFile.close();
}