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disable multiple assertions

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chhylp123
2023-08-17 19:58:35 -04:00
parent 64091a76a5
commit 858b95a3bb
3 changed files with 14 additions and 10 deletions
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5
CommandLines.cpp
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@@ -61,6 +61,7 @@ static ko_longopt_t long_options[] = {
{ "path-max", ko_required_argument, 346},
{ "path-min", ko_required_argument, 347},
{ "trio-dual", ko_no_argument, 348},
{ "ul-cut", ko_required_argument, 349},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -174,6 +175,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " --path-min FLOAT\n");
fprintf(stderr, " min path drop ratio [%.2g]; higher number may make the assembly cleaner\n", asm_opt->min_path_drop_rate);
fprintf(stderr, " but may lead to more misassemblies\n");
fprintf(stderr, " --ul-cut INT\n");
fprintf(stderr, " filter out <INT UL reads during the UL assembly [%d]\n", asm_opt->ul_min_base);
// fprintf(stderr, " --low-het enable it for genomes with very low het heterozygosity rate (<0.0001%%)\n");
fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n");
@@ -290,6 +293,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->hifi_pst_join = 1;
asm_opt->ul_pst_join = 1;
asm_opt->trio_cov_het_ovlp = -1;
asm_opt->ul_min_base = 0;
}
void destory_enzyme(enzyme* f)
@@ -835,6 +839,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 346) asm_opt->max_path_drop_rate = atof(opt.arg);
else if (c == 347) asm_opt->min_path_drop_rate = atof(opt.arg);
else if (c == 348) asm_opt->trio_cov_het_ovlp = 1;
else if (c == 349) asm_opt->ul_min_base = 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);
}