<commit_before>#include "config.h"
#include <cstdlib>
#include <iostream>
#include <string>
#include <fstream>
#include <sstream>
#include <cstring>

using namespace std;

//// parameters

// for bam file
int min_flank_length = 5;
int min_clip_length = 5;
int32_t average_read_length = 100;
int32_t min_bundle_gap = 50;
int min_num_hits_in_bundle = 20;
int32_t min_splice_boundary_hits = 1;
uint32_t min_mapping_quality = 1;
double max_indel_ratio = 0.2;
int32_t min_subregion_gap = 3;
int32_t min_subregion_length = 15;
double min_subregion_overlap = 2;
double min_average_overlap = 3.0;
int min_max_region_overlap = 5;
double min_region_coverage = 0.5;
int max_num_bundles = -1;
int tail_coverage = 8;
int slope_bin_size = 10;
int slope_bin_num = 30;
int slope_min_score = 1000;
double slope_min_sigma = 5.0;
int pseudo_length_count = 10;
bool use_paired_end = false;
int max_equations_each_iteration = 50;
double max_ignorable_edge_weight = 10.0;
double max_removable_edge_weight = 5.5;
double min_edge_weight = 2.9;
double min_transcript_coverage = 10.0;
double min_splice_graph_coverage = 20.0;
int min_boundary_length = 80;
int min_boundary_score = 1000;
double min_boundary_sigma = 4.0;
int32_t partial_exon_length = 100;

// for algorithm
double join_min_reliability = 0.6;
double infer_min_reliability = 0.6;
double infer_root_reliability = 0.4;
int max_dp_table_size = 10000;
int max_num_subsetsum_solutions = 10;
double max_equation_error_ratio = 0.1;<commit_msg>change default ignorable-weight to 5.0<commit_after>#include "config.h"
#include <cstdlib>
#include <iostream>
#include <string>
#include <fstream>
#include <sstream>
#include <cstring>

using namespace std;

//// parameters

// for bam file
int min_flank_length = 5;
int min_clip_length = 5;
int32_t average_read_length = 100;
int32_t min_bundle_gap = 50;
int min_num_hits_in_bundle = 20;
int32_t min_splice_boundary_hits = 1;
uint32_t min_mapping_quality = 1;
double max_indel_ratio = 0.2;
int32_t min_subregion_gap = 3;
int32_t min_subregion_length = 15;
double min_subregion_overlap = 2;
double min_average_overlap = 3.0;
int min_max_region_overlap = 5;
double min_region_coverage = 0.5;
int max_num_bundles = -1;
int tail_coverage = 8;
int slope_bin_size = 10;
int slope_bin_num = 30;
int slope_min_score = 1000;
double slope_min_sigma = 5.0;
int pseudo_length_count = 10;
bool use_paired_end = false;
int max_equations_each_iteration = 50;
double max_ignorable_edge_weight = 5.0;
double max_removable_edge_weight = 5.5;
double min_edge_weight = 2.9;
double min_transcript_coverage = 10.0;
double min_splice_graph_coverage = 20.0;
int min_boundary_length = 80;
int min_boundary_score = 1000;
double min_boundary_sigma = 4.0;
int32_t partial_exon_length = 100;

// for algorithm
double join_min_reliability = 0.6;
double infer_min_reliability = 0.6;
double infer_root_reliability = 0.4;
int max_dp_table_size = 10000;
int max_num_subsetsum_solutions = 10;
double max_equation_error_ratio = 0.1;
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{'dir': 'git-commits-cleaned', 'id': '462937', 'n_tokens_mistral': 1286, 'n_tokens_neox': 1120, 'n_words': 277}