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add "n-weight"

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chhylp123
2021-04-24 00:03:36 -04:00
parent 7b07e355b7
commit c972c64b39
5 changed files with 71 additions and 27 deletions
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10
CommandLines.cpp
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@@ -37,6 +37,7 @@ static ko_longopt_t long_options[] = {
{ "n-perturb", ko_required_argument, 323 },
{ "f-perturb", ko_required_argument, 324 },
{ "n-hap", ko_required_argument, 325 },
{ "n-weight", ko_required_argument, 326 },
{ 0, 0, 0 }
};
@@ -113,6 +114,10 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " --h1 FILEs file names of Hi-C R1 [r1_1.fq,r1_2.fq,...]\n");
fprintf(stderr, " --h2 FILEs file names of Hi-C R2 [r2_1.fq,r2_2.fq,...]\n");
fprintf(stderr, " --seed INT RNG seed [%lu]\n", asm_opt->seed);
fprintf(stderr, " --n-weight INT\n");
fprintf(stderr, " rounds of reweighting Hi-C links [%d]\n", asm_opt->n_weight);
fprintf(stderr, " --n-perturb INT\n");
fprintf(stderr, " rounds of perturbation [%d]\n", asm_opt->n_perturb);
fprintf(stderr, " --f-perturb FLOAT\n");
@@ -188,8 +193,9 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->polyploidy = 2;
asm_opt->trio_flag_occ_thres = 60;
asm_opt->seed = 11;
asm_opt->n_perturb = 50000;
asm_opt->n_perturb = 10000;
asm_opt->f_perturb = 0.1;
asm_opt->n_weight = 3;
}
void destory_enzyme(enzyme* f)
@@ -651,6 +657,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 323) asm_opt->n_perturb = atoi(opt.arg);
else if (c == 324) asm_opt->f_perturb = atof(opt.arg);
else if (c == 325) asm_opt->polyploidy = atoi(opt.arg);
else if (c == 326) asm_opt->n_weight = atoi(opt.arg);
else if (c == 'l')
{ ///0: disable purge_dup; 1: purge containment; 2: purge overlap
asm_opt->purge_level_primary = asm_opt->purge_level_trio = atoi(opt.arg);
@@ -682,6 +689,5 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
get_queries(argc, argv, &opt, asm_opt);
return check_option(asm_opt);
}