mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-07 16:48:11 +08:00
r852 -> hybrid correction
This commit is contained in:
chhylp123
+217
-195
@@ -1,195 +1,217 @@
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#ifndef __COMMAND_LINE_PARSER__
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#define __COMMAND_LINE_PARSER__
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#define __STDC_LIMIT_MACROS
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#include <pthread.h>
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#include <stdint.h>
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#define HA_VERSION "0.25.0-r726"
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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_F_PARTITION 0x800
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#define HA_F_FAST 0x1000
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#define HA_F_USKEW 0x2000
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#define HA_MIN_OV_DIFF 0.02 // min sequence divergence in an overlap
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#define MIN_N_CHAIN 100
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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 *fn_bin_poy;
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char *extract_list;
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enzyme *hic_reads[2];
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enzyme *hic_enzymes;
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enzyme *ar;
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enzyme *sec_in;
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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 ul_mer_length;
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int trans_mer_length;
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int bub_mer_length;
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int mz_win;
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int ul_mz_win;
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int trans_win;
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int mz_rewin;
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int ul_mz_rewin;
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int mz_sample_dist;
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int bf_shift;
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int max_kmer_cnt;
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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 b_low_cov;
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int b_high_cov;
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double m_rate;
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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 number_of_pround;
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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 max_short_ul_tip;
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int max_contig_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 purge_overlap_len_hic;
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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 hom_global_coverage_set;
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int pur_global_coverage;
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int bed_inconsist_rate;
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int hic_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_l2;
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float purge_simi_rate_l3;
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float purge_simi_thres;
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float trans_base_rate;
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float trans_base_rate_sec;
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float min_path_drop_rate;
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float max_path_drop_rate;
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// uint64_t path_clean_round;
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///float purge_simi_rate_hic;
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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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int hap_occ;
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int polyploidy;
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int trio_flag_occ_thres;
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uint64_t seed;
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int32_t n_perturb;
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double f_perturb;
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int32_t n_weight;
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uint32_t is_alt;
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uint64_t misjoin_len;
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uint64_t scffold;
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int32_t dp_min_len;
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float dp_e;
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int64_t hg_size;
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float kpt_rate;
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int64_t infor_cov, s_hap_cov, trio_cov_het_ovlp;
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double ul_error_rate, ul_error_rate_low, ul_error_rate_hpc;
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int32_t ul_ec_round;
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int32_t ul_mod;
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uint8_t is_dbg_het_cnt;
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uint8_t is_low_het_ul;
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uint8_t is_base_trans;
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uint8_t is_read_trans;
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uint8_t is_topo_trans;
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uint8_t is_bub_trans;
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uint8_t bin_only;
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int32_t ul_clean_round;
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int32_t prt_dbg_gfa;
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int32_t integer_correct_round;
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uint8_t dbg_ovec_cal;
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uint8_t hifi_pst_join, ul_pst_join;
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uint32_t ul_min_base;
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uint8_t self_scaf;
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uint64_t self_scaf_min;
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uint64_t self_scaf_reliable_min;
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int64_t self_scaf_gap_max;
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int64_t somatic_cov;
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char *telo_motif;
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int64_t telo_pen;
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int64_t telo_drop;
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int64_t telo_mic_sc;
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uint64_t is_ont;
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uint64_t is_sc;
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uint64_t chemical_cov;
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uint64_t chemical_flank;
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int64_t rl_cut;
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int64_t sc_cut;
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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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void ha_opt_update_cov_min(hifiasm_opt_t *opt, int hom_cov, int min_chain);
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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_reads[0] && opt->hic_reads[1]));
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}
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#endif
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#ifndef __COMMAND_LINE_PARSER__
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#define __COMMAND_LINE_PARSER__
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#define __STDC_LIMIT_MACROS
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#include <pthread.h>
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#include <stdint.h>
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#define HA_VERSION "0.25.0-r852"
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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_F_PARTITION 0x800
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#define HA_F_FAST 0x1000
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#define HA_F_USKEW 0x2000
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#define HA_MIN_OV_DIFF 0.02 // min sequence divergence in an overlap
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#define MIN_N_CHAIN 100
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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 *fn_bin_poy;
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char *fn_chr_bin;
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char *extract_list;
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enzyme *hic_reads[2];
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enzyme *hic_enzymes;
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enzyme *ar;
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enzyme *hf;
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enzyme *sec_in;
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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 ul_mer_length;
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int trans_mer_length;
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int bub_mer_length;
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int mz_win;
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int ul_mz_win;
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int trans_win;
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int mz_rewin;
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int ul_mz_rewin;
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int mz_sample_dist;
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int bf_shift;
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int max_kmer_cnt;
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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_ec_sec;
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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 b_low_cov;
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int b_high_cov;
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double m_rate;
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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 number_of_pround;
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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 max_short_ul_tip;
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int max_contig_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 purge_overlap_len_hic;
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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 hom_global_coverage_set;
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int pur_global_coverage;
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int bed_inconsist_rate;
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int hic_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_l2;
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float purge_simi_rate_l3;
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float purge_simi_thres;
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float trans_base_rate;
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float trans_base_rate_sec;
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float min_path_drop_rate;
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float max_path_drop_rate;
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// uint64_t path_clean_round;
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///float purge_simi_rate_hic;
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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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int hap_occ;
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int polyploidy;
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int trio_flag_occ_thres;
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uint64_t seed;
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int32_t n_perturb;
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double f_perturb;
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int32_t n_weight;
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uint32_t is_alt;
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uint64_t misjoin_len;
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uint64_t scffold;
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int32_t dp_min_len;
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float dp_e;
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int64_t hg_size;
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float kpt_rate;
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int64_t infor_cov, s_hap_cov, trio_cov_het_ovlp;
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double ul_error_rate, ul_error_rate_low, ul_error_rate_hpc;
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int32_t ul_ec_round;
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int32_t ul_mod;
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uint8_t is_dbg_het_cnt;
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uint8_t is_low_het_ul;
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uint8_t is_base_trans;
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uint8_t is_read_trans;
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uint8_t is_topo_trans;
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uint8_t is_bub_trans;
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uint8_t bin_only;
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int32_t ul_clean_round;
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int32_t prt_dbg_gfa;
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int32_t integer_correct_round;
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uint8_t dbg_ovec_cal;
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uint8_t hifi_pst_join, ul_pst_join;
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uint32_t ul_min_base;
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uint8_t self_scaf;
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uint64_t self_scaf_min;
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uint64_t self_scaf_reliable_min;
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int64_t self_scaf_gap_max;
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int64_t somatic_cov;
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char *telo_motif;
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int64_t telo_pen;
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int64_t telo_drop;
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int64_t telo_mic_sc;
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uint64_t is_ont;
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uint64_t is_sc;
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uint64_t chemical_cov;
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uint64_t chemical_flank;
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int64_t rl_cut;
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int64_t sc_cut;
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uint8_t gpath;
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uint64_t hf_rate;///cannot be larger than 128?
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uint64_t hf_rate_max;///cannot be larger than 128?
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uint64_t ont_rate;///cannot be 0, should be 1 in anyway
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int64_t het_cov_set;
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int64_t restart;
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int64_t hf_cutoff;
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uint8_t write_pos_idx;
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int hom_cov_0;
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int het_cov_0;
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int max_n_chain_0; // fall-back max number of chains to consider
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int64_t hmo_cov_ss;
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int64_t het_cov_ss;
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int64_t chn_occ;
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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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void ha_opt_update_cov_min(hifiasm_opt_t *opt, int hom_cov, int min_chain);
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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_reads[0] && opt->hic_reads[1]));
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}
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#endif
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