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r342-misjoin

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chhylp123
2021-06-19 14:09:09 -04:00
parent e3b721c29a
commit 5a400af39d
9 changed files with 845 additions and 22 deletions
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6
CommandLines.cpp
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@@ -38,6 +38,7 @@ static ko_longopt_t long_options[] = {
{ "f-perturb", ko_required_argument, 324 },
{ "n-hap", ko_required_argument, 325 },
{ "n-weight", ko_required_argument, 326 },
{ "l-msjoin", ko_required_argument, 327 },
{ 0, 0, 0 }
};
@@ -122,7 +123,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " rounds of perturbation [%d]\n", asm_opt->n_perturb);
fprintf(stderr, " --f-perturb FLOAT\n");
fprintf(stderr, " fraction to flip for perturbation [%.3g]\n", asm_opt->f_perturb);
fprintf(stderr, " --l-msjoin INT\n");
fprintf(stderr, " detect misjoined unitigs of >=INT in size; 0 to disable [%lu]\n", asm_opt->misjoin_len);
fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n");
fprintf(stderr, "See `man ./hifiasm.1' for detailed description of these command-line options.\n");
@@ -196,6 +198,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->f_perturb = 0.1;
asm_opt->n_weight = 3;
asm_opt->is_alt = 0;
asm_opt->misjoin_len = 500000;
}
void destory_enzyme(enzyme* f)
@@ -658,6 +661,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
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 == 327) asm_opt->misjoin_len = atol(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);