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dp opt

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chhylp123
2021-08-12 11:16:10 -04:00
parent 6ea66e1290
commit bfff640a82
8 changed files with 646 additions and 113 deletions
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8
CommandLines.cpp
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@@ -40,6 +40,9 @@ static ko_longopt_t long_options[] = {
{ "n-weight", ko_required_argument, 326 },
{ "l-msjoin", ko_required_argument, 327 },
{ "purge-max", ko_required_argument, 328 },
{ "fast", ko_no_argument, 329 },
{ "dp-er", ko_required_argument, 330},
{ "max-kocc", ko_required_argument, 331},
{ 0, 0, 0 }
};
@@ -207,6 +210,8 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->is_alt = 0;
asm_opt->misjoin_len = 500000;
asm_opt->scffold = 0;
asm_opt->dp_min_len = 2000;
asm_opt->dp_e = 0.0025;
}
void destory_enzyme(enzyme* f)
@@ -677,6 +682,9 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
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 == 328) asm_opt->pur_global_coverage = atoi(opt.arg);
else if (c == 329) asm_opt->flag |= HA_F_FAST;
else if (c == 330) asm_opt->dp_e = atof(opt.arg);
else if (c == 331) asm_opt->max_kmer_cnt = 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);