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global-types-and-parameters_MitoGeneExtractor.h
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global-types-and-parameters_MitoGeneExtractor.h
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#include <iostream>
#include <string>
#include <vector>
//#include "faststring2.h"
#define DEBUG
#define PROGNAME "MitoGeneExtractor"
#define VERSION "1.9.5"
#define macromax(x,y) ((x)<(y) ? (y) : (x))
#define macromin(x,y) ((x)<(y) ? (x) : (y))
#ifdef DEBUG
#define DEBUGOUT1(x) std::cerr << x << std::endl;
#define DEBUGOUT2(x,y) std::cerr << x << y << std::endl;
#define DEBUGOUT3(x,y,z) std::cerr << x << y << z << std::endl;
#define DEBUGOUT4(x,y,z,w) std::cerr << x << y << z << w << std::endl;
#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(int);
void init_param();
void read_and_init_parameters(int argc, char** argv);
void print_parameters(std::ostream &os, const char *s);
extern std::vector<std::string> global_input_dna_fasta_filenames;
extern std::vector<std::string> global_input_dna_fastq_filenames;
extern std::string global_input_prot_reference_sequence;
extern std::string global_tmp_directory;
extern unsigned global_verbosity;
extern unsigned global_num_bp_beyond_exonerate_alignment_if_at_start_or_end;
extern std::string global_exonerate_binary;
extern std::string global_vulgar_file;
extern std::string global_alignment_output_file;
extern float global_consensus_threshold;
extern std::string global_consensus_sequence_output_filename;
extern char global_include_frameshift_alignments;
extern char global_notinclude_gap_alignments;
extern char global_include_only_gap_alignments;
extern char global_include_double_hits;
extern float global_relative_score_threshold;
extern char global_genetic_code_number;
extern int global_frameshift_penalty;
extern char global_run_mode; // Exonerate run mode. Supported modes: 'd': dry run.
extern unsigned global_minimum_seq_coverage_uppercase;
extern unsigned global_minimum_seq_coverage_total;
extern unsigned global_exonerate_score_threshold;
extern int global_gap_frameshift_mode;
extern int global_report_gap_mode;
extern bool global_keep_concatenated_input_file;
extern unsigned global_ends_width;
extern unsigned global_weight_fraction_in_ends;
extern bool global_treat_references_as_individual;
//extern bool global_report_internal_gaps_as_tilde;