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running time bug fixed

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chhylp123
2026-02-16 10:46:28 -05:00
parent 53e1b150c3
commit 86311effb9
6 changed files with 529 additions and 59 deletions
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CommandLines.cpp
+10 -2
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@@ -88,6 +88,8 @@ static ko_longopt_t long_options[] = {
{ "resume", ko_no_argument, 370},
{ "flt-kocc", ko_required_argument, 371},
{ "chn-occ", ko_required_argument, 372},
{ "dbg-in1", ko_required_argument, 373},
{ "dbg-in2", ko_required_argument, 374},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -415,6 +417,9 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->hmo_cov_ss = -1;
asm_opt->het_cov_ss = -1;
asm_opt->chn_occ = 2;
asm_opt->dbg_run_1 = NULL;
asm_opt->dbg_run_2 = NULL;
}
void destory_enzyme(enzyme* f)
@@ -1075,8 +1080,11 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
fprintf(stderr, "[ERROR] chain cutoff should be > 0 (--chn-occ)");
return 1;
}
}
else if (c == 'l') { ///0: disable purge_dup; 1: purge containment; 2: purge overlap
} else if (c == 373) {
asm_opt->dbg_run_1 = opt.arg;
} else if (c == 374) {
asm_opt->dbg_run_2 = 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);
}
else if (c == 's') asm_opt->purge_simi_rate_l2 = asm_opt->purge_simi_rate_l3 = atof(opt.arg);