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CommandLines.h
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CommandLines.h
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#ifndef __COMMAND_LINE_PARSER__
#define __COMMAND_LINE_PARSER__
#include <pthread.h>
#define HA_VERSION "0.13-r308"
#define HAMT_VERSION "0.3-r074"
// #define VERBOSE 1
extern int VERBOSE; // expose to cli
#define HA_F_NO_HPC 0x1
#define HA_F_NO_KMER_FLT 0x2
#define HA_F_VERBOSE_GFA 0x4
#define HA_F_WRITE_EC 0x8
#define HA_F_WRITE_PAF 0x10
#define HA_F_SKIP_TRIOBIN 0x20
#define HA_F_PURGE_CONTAIN 0x40
#define HA_F_PURGE_JOIN 0x80
#define HA_F_BAN_POST_JOIN 0x100
#define HA_F_BAN_ASSEMBLY 0x200
#define HA_F_HIGH_HET 0x400
#define HA_MIN_OV_DIFF 0.02 // min sequence divergence in an overlap
typedef struct {
int flag;
int num_reads;
char** read_file_names;
char* output_file_name;
char* required_read_name;
char *fn_bin_yak[2];
char *fn_bin_list[2];
char *extract_list;
int extract_iter;
int thread_num;
int k_mer_length;
int mz_win;
int bf_shift;
double high_factor; // coverage cutoff set to high_factor*hom_cov
double max_ov_diff_ec;
double max_ov_diff_final;
int hom_cov;
int het_cov;
int max_n_chain; // fall-back max number of chains to consider
int min_hist_kmer_cnt;
int load_index_from_disk;
int write_index_to_disk;
int number_of_round;
int adapterLen;
int clean_round;
int roundID;
int max_hang_Len;
int gap_fuzz;
int min_overlap_Len;
int min_overlap_coverage;
int max_short_tip;
int min_cnt;
int mid_cnt;
int purge_level_primary;
int purge_level_trio;
int purge_overlap_len;
int recover_atg_cov_min;
int recover_atg_cov_max;
int hom_global_coverage;
int bed_inconsist_rate;
float max_hang_rate;
float min_drop_rate;
float max_drop_rate;
float purge_simi_rate;
long long small_pop_bubble_size;
long long large_pop_bubble_size;
long long num_bases;
long long num_corrected_bases;
long long num_recorrected_bases;
long long mem_buf;
long long coverage;
// hamt
int is_disable_read_selection;
int mode_read_kmer_profile;
int readselection_sort_order; // experimental, 1 for smallestFirst, 2 for largestFirst, 0 to force disable it (note that we still go through loading all reads + sorting, just don't use the info when annotation mask_readnorm)
char *bin_base_name; // -B
char *probebin_base_name; //--probe-gfa
int is_ignore_ovlp_cnt; // experimental, do preovec read selection even if the whole read set looks practical
int preovec_coverage;
int is_dump_read_mask;
int is_dump_read_names;
int is_use_exp_graph_cleaning;
int is_dump_ovec_error_count;
int lowq_thre_10;
int lowq_thre_5;
int lowq_thre_3;
int write_debug_gfa;
int write_new_graph_bins;
int use_ha_bin; //
int is_final_round;
int is_mode_low_cov;
int is_dump_relevant_reads; FILE *fp_relevant_reads;
// hifiasm_argcv_t *argcv;
// hamt, graph cleaning control
int gc_superbubble_tig_max_length;
int gc_tangle_max_tig;
int mode_coasm;
int is_aggressive;
int do_probe_gfa;
int no_containedreads_heuristics;
int write_binning_fasta;
// hamt, multiprocessing context for get_specific_overlap's binary search
int get_specific_overlap_is_use_bf;
// tsne in binning
int tsne_perplexity;
int tsne_randomseed;
float tsne_neigh_dist;
int no_post_assembly_binning;
// end of hamt
} hifiasm_opt_t;
typedef struct {
int ha_argc;
char **ha_argv;
} hifiasm_argcv_t; // hamt
extern hifiasm_opt_t asm_opt;
extern hifiasm_argcv_t asm_argcv;
void init_opt(hifiasm_opt_t* asm_opt);
void destory_opt(hifiasm_opt_t* asm_opt);
void ha_opt_reset_to_round(hifiasm_opt_t* asm_opt, int round);
void ha_opt_update_cov(hifiasm_opt_t *opt, int hom_cov);
int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt);
double Get_T(void);
double Get_U(void);
static inline int ha_opt_triobin(const hifiasm_opt_t *opt)
{
return ((opt->fn_bin_yak[0] && opt->fn_bin_yak[1]) || (opt->fn_bin_list[0] && opt->fn_bin_list[1]));
}
#endif