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chhylp123
2024-11-12 23:53:29 -05:00
parent 6de4e14782
commit 80fa5ed436
11 changed files with 1211 additions and 135 deletions
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8
CommandLines.cpp
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@@ -72,6 +72,7 @@ static ko_longopt_t long_options[] = {
{ "telo-s", ko_required_argument, 357},
{ "ctg-n", ko_required_argument, 358},
{ "ont", ko_no_argument, 359},
{ "sc-n", ko_no_argument, 360},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -340,7 +341,8 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->telo_mic_sc = 500;
asm_opt->is_ont = 0;
}
asm_opt->is_sc = 0;
}
void destory_enzyme(enzyme* f)
{
@@ -912,7 +914,9 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 357) asm_opt->telo_mic_sc = atol(opt.arg);
else if (c == 358) asm_opt->max_contig_tip = atol(opt.arg);
else if (c == 359) {
asm_opt->is_ont = 1; asm_opt->max_ov_diff_ec = 0.07;
asm_opt->is_ont = 1; asm_opt->max_ov_diff_ec = 0.07; ///asm_opt->mz_win = 37; asm_opt->k_mer_length = 37;
} else if (c == 360) {
asm_opt->is_sc = 1;
} 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);
}