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global-types-and-parameters.h
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global-types-and-parameters.h
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/* BaitFisher (version 1.2.8) a program for designing DNA target enrichment baits
* BaitFilter (version 1.0.6) a program for selecting optimal bait regions
* Copyright 2013-2017 by Christoph Mayer
*
* This source file is part of the BaitFisher-package.
*
* 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 3 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 BaitFisher. If not, see <http://www.gnu.org/licenses/>.
*
*
* For any enquiries send an Email to Christoph Mayer
*
* When publishing work that is based on the results please cite:
* Mayer et al. 2016: BaitFisher: A software package for multi-species target DNA enrichment probe design
*
*/
#ifndef GLOBAL_TYPES_AND_PARAMETERS_H
#define GLOBAL_TYPES_AND_PARAMETERS_H
#include <cstdio>
#include <iostream>
#include <vector>
#include <string>
#include <cstring>
#include "faststring2.h"
#include <climits>
#include <fstream>
#define DEBUG
#define PROGNAME "Bait-Filter"
#define VERSION "1.0.6"
extern faststring global_bait_filename; //
extern char global_mode; //
extern faststring global_blast_exe; //
extern faststring global_output_filename;
extern double global_blast_min_hit_coverage_of_bait;
extern double global_blast_max_first_hit_evalue;
extern double global_blast_max_second_hit_evalue;
extern faststring global_blast_db; //
extern faststring global_blast_extra_commandline;
extern faststring global_blast_evalue_commandline;
extern unsigned global_thinning_step_width;
extern bool global_use_GUI;
extern unsigned global_conversion_mode;
extern faststring global_ProbeID_prefix;
extern unsigned global_verbosity;
extern faststring global_blast_result_file;
extern bool skip_blast;
#define macromax(x,y) ((x)<(y) ? (y) : (x))
#define macromin(x,y) ((x)<(y) ? (x) : (y))
#ifdef DEBUG
#define DEBUGOUT1(x) std::cerr << x << '\n';
#define DEBUGOUT2(x,y) std::cerr << x << y << '\n';
#define DEBUGOUT3(x,y,z) std::cerr << x << y << z << '\n';
#define DEBUGOUT4(x,y,z,w) std::cerr << x << y << z << w << '\n';
#else
#define DEBUGOUT1(x)
#define DEBUGOUT2(x,y)
#define DEBUGOUT3(x,y,z)
#define DEBUGOUT4(x,y,z,w)
#endif
void good_bye_and_exit(FILE *of, int);
void good_bye_and_exit(std::ostream&, int);
void init_param();
void read_and_init_parameters(int argc, char** argv, std::ostream &);
void print_parameters(FILE*, const char *s);
void print_parameters(std::ostream&, const char *s);
void print_calling_command_line(FILE*,unsigned, char**);
void print_calling_command_line(std::ostream&,unsigned, char**);
#endif