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https://github.com/chhylp123/hifiasm.git
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65 lines
1.5 KiB
C
65 lines
1.5 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 "0.3.0-dirty-r205"
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#define VERBOSE 0
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typedef struct {
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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* pat_index;
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char* mat_index;
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int thread_num;
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int k_mer_length;
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int mz_win;
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int bf_shift;
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int no_HPC;
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int no_kmer_flt;
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float high_factor; // coverage cutoff set to high_factor*hom_cov
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int max_n_chain; // fall-back max number of chains to consider
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int k_mer_min_freq;
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int k_mer_max_freq;
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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 verbose_gfa;
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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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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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#endif
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