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add new options for ont assembly

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chhylp123
2025-03-18 12:29:48 -04:00
parent b3b18ab1d0
commit ec9a8b222d
3 changed files with 38 additions and 2 deletions
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CommandLines.cpp
+16
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@@ -79,6 +79,8 @@ static ko_longopt_t long_options[] = {
{ "chem-c", ko_required_argument, 361},
{ "chem-f", ko_required_argument, 362},
{ "ul-m", ko_required_argument, 363},
{ "rl-cut", ko_required_argument, 364},
{ "sc-cut", ko_required_argument, 365},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -228,6 +230,10 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " detect chimeric reads with <=INT other reads support [%lu]\n", asm_opt->chemical_cov);
fprintf(stderr, " --chem-f INT\n");
fprintf(stderr, " length of flanking regions for chimeric read detection [%lu]\n", asm_opt->chemical_flank);
fprintf(stderr, " --rl-cut INT\n");
fprintf(stderr, " filter out ONT simplex reads shorter than <INT> for assembly [%ld]\n", asm_opt->rl_cut);
fprintf(stderr, " --sc-cut INT\n");
fprintf(stderr, " filter out ONT simplex reads with a mean base quality score below <INT> [%ld]\n", asm_opt->sc_cut);
fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n");
@@ -364,6 +370,9 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->chemical_cov = 1;
asm_opt->chemical_flank = 256;
asm_opt->ul_mod = 0;
asm_opt->rl_cut = 1000;
asm_opt->sc_cut = 10;
}
void destory_enzyme(enzyme* f)
@@ -990,6 +999,10 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
} else if (c == 363) {
asm_opt->ul_mod = atol(opt.arg);
**/
} else if (c == 364) {
asm_opt->rl_cut = atol(opt.arg);
} else if (c == 365) {
asm_opt->sc_cut = 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);
}
@@ -1027,6 +1040,9 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
// fprintf(stderr, "[M::%s::] post join::%u\n", __func__, (uint32_t)(!(asm_opt->flag & HA_F_BAN_POST_JOIN)));
// exit(1);
if(!(asm_opt->is_ont)) {
asm_opt->rl_cut = -1; asm_opt->sc_cut = 1;
}
return check_option(asm_opt);
}