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trio-dual/bug for hic phasing

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chhylp123
2023-05-31 14:54:50 -04:00
parent 44475e2665
commit adeb2c603d
7 changed files with 259 additions and 6 deletions
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5
CommandLines.cpp
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@@ -60,6 +60,7 @@ static ko_longopt_t long_options[] = {
{ "dbg-ovec", ko_no_argument, 345},
{ "path-max", ko_required_argument, 346},
{ "path-min", ko_required_argument, 347},
{ "trio-dual", ko_no_argument, 348},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -129,6 +130,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " --t-occ INT\n");
fprintf(stderr, " forcedly remove unitigs with >INT unexpected haplotype-specific reads;\n");
fprintf(stderr, " ignore graph topology; [%d]\n", asm_opt->trio_flag_occ_thres);
fprintf(stderr, " --trio-dual utilize homology information to correct trio phasing errors\n");
fprintf(stderr, " Purge-dups:\n");
fprintf(stderr, " -l INT purge level. 0: no purging; 1: light; 2/3: aggressive [0 for trio; 3 for unzip]\n");
@@ -286,6 +289,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->max_path_drop_rate = 0.6;
asm_opt->hifi_pst_join = 1;
asm_opt->ul_pst_join = 1;
asm_opt->trio_cov_het_ovlp = -1;
}
void destory_enzyme(enzyme* f)
@@ -830,6 +834,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
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 == 348) asm_opt->trio_cov_het_ovlp = 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);
}