mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
110 lines
2.6 KiB
C
110 lines
2.6 KiB
C
#ifndef __COMMAND_LINE_PARSER__
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#define __COMMAND_LINE_PARSER__
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#include <pthread.h>
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#define HA_VERSION "0.13-r308"
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#define VERBOSE 0
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#define HA_F_NO_HPC 0x1
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#define HA_F_NO_KMER_FLT 0x2
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#define HA_F_VERBOSE_GFA 0x4
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#define HA_F_WRITE_EC 0x8
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#define HA_F_WRITE_PAF 0x10
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#define HA_F_SKIP_TRIOBIN 0x20
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#define HA_F_PURGE_CONTAIN 0x40
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#define HA_F_PURGE_JOIN 0x80
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#define HA_F_BAN_POST_JOIN 0x100
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#define HA_F_BAN_ASSEMBLY 0x200
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#define HA_F_HIGH_HET 0x400
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#define HA_MIN_OV_DIFF 0.02 // min sequence divergence in an overlap
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typedef struct{
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int *l, n;
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char **a;
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}enzyme;
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typedef struct {
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int flag;
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int num_reads;
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char** read_file_names;
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char* output_file_name;
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char* required_read_name;
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char *fn_bin_yak[2];
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char *fn_bin_list[2];
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char *extract_list;
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char *hic_files[2];
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enzyme *hic_enzymes;
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int extract_iter;
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int thread_num;
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int k_mer_length;
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int hic_mer_length;
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int bub_mer_length;
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int mz_win;
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int bf_shift;
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double high_factor; // coverage cutoff set to high_factor*hom_cov
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double max_ov_diff_ec;
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double max_ov_diff_final;
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int hom_cov;
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int het_cov;
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int max_n_chain; // fall-back max number of chains to consider
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int min_hist_kmer_cnt;
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int load_index_from_disk;
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int write_index_to_disk;
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int number_of_round;
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int adapterLen;
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int clean_round;
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int roundID;
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int max_hang_Len;
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int gap_fuzz;
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int min_overlap_Len;
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int min_overlap_coverage;
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int max_short_tip;
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int min_cnt;
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int mid_cnt;
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int purge_level_primary;
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int purge_level_trio;
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int purge_overlap_len;
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int recover_atg_cov_min;
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int recover_atg_cov_max;
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int hom_global_coverage;
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int bed_inconsist_rate;
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float max_hang_rate;
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float min_drop_rate;
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float max_drop_rate;
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float purge_simi_rate;
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long long small_pop_bubble_size;
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long long large_pop_bubble_size;
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long long num_bases;
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long long num_corrected_bases;
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long long num_recorrected_bases;
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long long mem_buf;
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long long coverage;
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} hifiasm_opt_t;
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extern hifiasm_opt_t asm_opt;
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void init_opt(hifiasm_opt_t* asm_opt);
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void destory_opt(hifiasm_opt_t* asm_opt);
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void ha_opt_reset_to_round(hifiasm_opt_t* asm_opt, int round);
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void ha_opt_update_cov(hifiasm_opt_t *opt, int hom_cov);
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int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt);
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double Get_T(void);
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static inline int ha_opt_triobin(const hifiasm_opt_t *opt)
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{
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return ((opt->fn_bin_yak[0] && opt->fn_bin_yak[1]) || (opt->fn_bin_list[0] && opt->fn_bin_list[1]));
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}
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static inline int ha_opt_hic(const hifiasm_opt_t *opt)
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{
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return ((opt->hic_files[0] && opt->hic_files[1]));
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}
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#endif
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