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path-max and path-min to avoid misassemblies

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chhylp123
2023-03-13 11:13:57 -04:00
parent 3407c7029e
commit f67faa9c34
4 changed files with 34 additions and 9 deletions
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13
CommandLines.cpp
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@@ -58,6 +58,9 @@ static ko_longopt_t long_options[] = {
{ "prt-raw", ko_no_argument, 343},
{ "integer-correct", ko_required_argument, 344},
{ "dbg-ovec", ko_no_argument, 345},
{ "path-max", ko_required_argument, 346},
{ "path-min", ko_required_argument, 347},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -160,6 +163,12 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " error rate of Ultra-Long reads [%.3g]\n", asm_opt->ul_error_rate);
fprintf(stderr, " --ul-tip INT\n");
fprintf(stderr, " remove tip unitigs composed of <=INT reads for the UL assembly [%d]\n", asm_opt->max_short_ul_tip);
fprintf(stderr, " --path-max FLOAT\n");
fprintf(stderr, " max path drop ratio [%.2g]; higher number may make the assembly cleaner\n", asm_opt->max_path_drop_rate);
fprintf(stderr, " but may lead to more misassemblies\n");
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, " --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");
@@ -271,6 +280,8 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->prt_dbg_gfa = 0;
asm_opt->integer_correct_round = 0;
asm_opt->dbg_ovec_cal = 0;
asm_opt->min_path_drop_rate = 0.2;
asm_opt->max_path_drop_rate = 0.6;
}
void destory_enzyme(enzyme* f)
@@ -807,6 +818,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 343) asm_opt->prt_dbg_gfa = 1;
else if (c == 344) asm_opt->integer_correct_round = atol(opt.arg);
else if (c == 345) asm_opt->dbg_ovec_cal = 1;
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 == 'l') { ///0: disable purge_dup; 1: purge containment; 2: purge overlap
asm_opt->purge_level_primary = asm_opt->purge_level_trio = atoi(opt.arg);
}