mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
251 lines
8.0 KiB
C++
251 lines
8.0 KiB
C++
#include "CommandLines.h"
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#include <zlib.h>
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#include <stdlib.h>
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#include <stdio.h>
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#include "ketopt.h"
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#include <sys/time.h>
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#define VERSION "0.1.0"
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#define DEFAULT_OUTPUT "hifiasm.asm"
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hifiasm_opt_t asm_opt;
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double Get_T(void)
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{
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struct timeval t;
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gettimeofday(&t, NULL);
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return t.tv_sec+t.tv_usec/1000000.0;
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}
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void Print_H(hifiasm_opt_t* asm_opt)
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{
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fprintf(stderr, "Usage: hifiasm [options] <in_1.fq> <in_2.fq> <...>\n");
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fprintf(stderr, "Options:\n");
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fprintf(stderr, " -o FILE prefix of output files [%s]\n", asm_opt->output_file_name);
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fprintf(stderr, " -t INT number of threads [%d]\n", asm_opt->thread_num);
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fprintf(stderr, " -r INT round of correction [%d]\n", asm_opt->number_of_round);
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fprintf(stderr, " -a INT round of assembly cleaning [%d]\n", asm_opt->clean_round);
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fprintf(stderr, " -k INT k-mer length [%d] (must be < 64)\n", asm_opt->k_mer_length);
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///fprintf(stderr, " -w write all overlaps to disk, can accelerate assembly next time [%d]\n", asm_opt->write_index_to_disk);
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///fprintf(stderr, " -l load all overlaps from disk, can avoid overlap calculation [%d]\n", asm_opt->load_index_from_disk);
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///fprintf(stderr, " -i ignore saved overlaps in *.ovlp*.bin files\n");
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fprintf(stderr, " -i ignore saved overlaps in *.ovlp* files\n");
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fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen);
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fprintf(stderr, " -p INT size of popped bubbles [%lld]\n", asm_opt->pop_bubble_size);
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fprintf(stderr, " -x FLOAT max overlap drop ratio [%.2g]\n", asm_opt->max_drop_rate);
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fprintf(stderr, " -y FLOAT min overlap drop ratio [%.2g]\n", asm_opt->min_drop_rate);
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fprintf(stderr, " -v show version number\n");
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fprintf(stderr, " -h show help information\n");
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fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n");
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}
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void init_opt(hifiasm_opt_t* asm_opt)
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{
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asm_opt->num_reads = 0;
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asm_opt->read_file_names = NULL;
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asm_opt->output_file_name = (char*)(DEFAULT_OUTPUT);
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asm_opt->required_read_name = NULL;
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asm_opt->thread_num = 1;
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asm_opt->k_mer_length = 40;
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asm_opt->k_mer_min_freq = 3;
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asm_opt->k_mer_max_freq = 66;
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asm_opt->load_index_from_disk = 1;
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asm_opt->write_index_to_disk = 1;
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asm_opt->number_of_round = 2;
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asm_opt->adapterLen = 0;
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asm_opt->clean_round = 4;
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asm_opt->complete_threads = 0;
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asm_opt->pop_bubble_size = 100000;
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asm_opt->min_drop_rate = 0.2;
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asm_opt->max_drop_rate = 0.8;
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}
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void destory_opt(hifiasm_opt_t* asm_opt)
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{
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if(asm_opt->read_file_names != NULL)
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{
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free(asm_opt->read_file_names);
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}
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}
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void clear_opt(hifiasm_opt_t* asm_opt, int last_round)
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{
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asm_opt->complete_threads = 0;
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asm_opt->num_bases = 0;
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asm_opt->num_corrected_bases = 0;
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asm_opt->num_recorrected_bases = 0;
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asm_opt->roundID = asm_opt->number_of_round - last_round;
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}
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int check_option(hifiasm_opt_t* asm_opt)
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{
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if(asm_opt->read_file_names == NULL || asm_opt->num_reads == 0)
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{
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fprintf(stderr, "[ERROR] missing input: please specify a read file\n");
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return 0;
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}
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if(asm_opt->output_file_name == NULL)
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{
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fprintf(stderr, "[ERROR] missing output: please specify the output name\n");
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return 0;
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}
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if(asm_opt->thread_num < 1)
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{
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fprintf(stderr, "[ERROR] the number of threads must be > 0\n");
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return 0;
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}
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if(asm_opt->number_of_round < 1)
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{
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fprintf(stderr, "[ERROR] the number of rounds for correction must be > 0\n");
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return 0;
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}
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if(asm_opt->clean_round < 1)
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{
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fprintf(stderr, "[ERROR] the number of rounds for assembly cleaning must be > 0\n");
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return 0;
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}
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if(asm_opt->adapterLen < 0)
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{
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fprintf(stderr, "[ERROR] the length of removed adapters must be >= 0\n");
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return 0;
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}
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if(asm_opt->k_mer_length >= 64)
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{
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fprintf(stderr, "[ERROR] the length of k_mer must be < 64\n");
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return 0;
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}
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if(asm_opt->max_drop_rate < 0 || asm_opt->max_drop_rate >= 1 )
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{
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fprintf(stderr, "[ERROR] max overlap drop ratio must be [0.0, 1.0)\n");
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return 0;
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}
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if(asm_opt->min_drop_rate < 0 || asm_opt->min_drop_rate >= 1)
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{
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fprintf(stderr, "[ERROR] min overlap drop ratio must be [0.0, 1.0)\n");
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return 0;
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}
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if(asm_opt->max_drop_rate <= asm_opt->min_drop_rate)
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{
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fprintf(stderr, "[ERROR] min overlap drop ratio must be less than max overlap drop ratio\n");
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return 0;
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}
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if(asm_opt->pop_bubble_size < 0)
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{
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fprintf(stderr, "[ERROR] the size of popped bubbles must be >= 0\n");
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return 0;
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}
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// fprintf(stderr, "input file num: %d\n", asm_opt->num_reads);
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// fprintf(stderr, "output file: %s\n", asm_opt->output_file_name);
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// fprintf(stderr, "number of threads: %d\n", asm_opt->thread_num);
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// fprintf(stderr, "number of rounds for correction: %d\n", asm_opt->number_of_round);
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// fprintf(stderr, "number of rounds for assembly cleaning: %d\n", asm_opt->clean_round);
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// fprintf(stderr, "length of removed adapters: %d\n", asm_opt->adapterLen);
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// fprintf(stderr, "length of k_mer: %d\n", asm_opt->k_mer_length);
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// fprintf(stderr, "min overlap drop ratio: %.2g\n", asm_opt->min_drop_rate);
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// fprintf(stderr, "max overlap drop ratio: %.2g\n", asm_opt->max_drop_rate);
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// fprintf(stderr, "size of popped bubbles: %lld\n", asm_opt->pop_bubble_size);
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return 1;
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}
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void get_queries(int argc, char *argv[], ketopt_t* opt, hifiasm_opt_t* asm_opt)
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{
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if(opt->ind == argc)
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{
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return;
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}
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asm_opt->num_reads = argc - opt->ind;
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asm_opt->read_file_names = (char**)malloc(sizeof(char*)*asm_opt->num_reads);
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long long i;
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gzFile dfp;
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for (i = 0; i < asm_opt->num_reads; i++)
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{
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asm_opt->read_file_names[i] = argv[i + opt->ind];
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dfp = gzopen(asm_opt->read_file_names[i], "r");
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if (dfp == 0)
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{
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fprintf(stderr, "[ERROR] Cannot find the input read file: %s\n",
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asm_opt->read_file_names[i]);
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exit(0);
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}
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gzclose(dfp);
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}
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}
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int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
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{
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ketopt_t opt = KETOPT_INIT;
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int c;
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while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:lwm:n:r:a:b:z:x:y:p:i", 0)) >= 0) {
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if (c == 'h')
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{
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Print_H(asm_opt);
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return 0;
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}
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else if (c == 'v')
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{
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fprintf(stderr, "[Version] %s\n", VERSION);
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return 0;
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}
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else if (c == 't') asm_opt->thread_num = atoi(opt.arg);
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else if (c == 'o') asm_opt->output_file_name = opt.arg;
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else if (c == 'n') asm_opt->k_mer_min_freq = atoi(opt.arg);
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else if (c == 'm') asm_opt->k_mer_max_freq = atoi(opt.arg);
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else if (c == 'r') asm_opt->number_of_round = atoi(opt.arg);
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else if (c == 'k') asm_opt->k_mer_length = atoi(opt.arg);
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else if (c == 'i') asm_opt->load_index_from_disk = 0;
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else if (c == 'l') asm_opt->load_index_from_disk = 1;
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else if (c == 'w') asm_opt->write_index_to_disk = 1;
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else if (c == 'a') asm_opt->clean_round = atoi(opt.arg);
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else if (c == 'z') asm_opt->adapterLen = atoi(opt.arg);
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else if (c == 'b') asm_opt->required_read_name = opt.arg;
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else if (c == 'x') asm_opt->max_drop_rate = atof(opt.arg);
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else if (c == 'y') asm_opt->min_drop_rate = atof(opt.arg);
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else if (c == 'p') asm_opt->pop_bubble_size = atoll(opt.arg);
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else if (c == ':')
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{
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fprintf(stderr, "[ERROR] missing option argument in \"%s\"\n", argv[opt.i - 1]);
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return 0;
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}
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else if (c == '?')
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{
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fprintf(stderr, "[ERROR] unknown option in \"%s\"\n", argv[opt.i - 1]);
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return 0;
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}
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}
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if (argc == 1)
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{
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Print_H(asm_opt);
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return 0;
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}
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get_queries(argc, argv, &opt, asm_opt);
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return check_option(asm_opt);
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}
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