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backup r321

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chhylp123
2021-04-01 21:02:57 -04:00
parent 0605aa1961
commit 46e899bbae
11 changed files with 1494 additions and 401 deletions
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CommandLines.cpp
+16 -1
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@@ -32,6 +32,8 @@ static ko_longopt_t long_options[] = {
{ "b-cov", ko_required_argument, 317 },
{ "h-cov", ko_required_argument, 318 },
{ "m-rate", ko_required_argument, 319 },
{ "b-partition", ko_no_argument, 320 },
{ "t-occ", ko_required_argument, 321 },
{ 0, 0, 0 }
};
@@ -87,6 +89,9 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -d INT upper bound of the binned k-mer's frequency [%d]\n", asm_opt->mid_cnt);
fprintf(stderr, " -3 FILE list of hap1/paternal read names []\n");
fprintf(stderr, " -4 FILE list of hap2/maternal read names []\n");
fprintf(stderr, " --t-occ INT\n");
fprintf(stderr, " force remove unitigs with >INT unexpected haplotype-specific reads;\n");
fprintf(stderr, " ignore graph topology; [%d]\n", asm_opt->trio_flag_occ_thres);
fprintf(stderr, " Purge-dups:\n");
fprintf(stderr, " -l INT purge level. 0: no purging; 1: light; 2/3: aggressive [0 for trio; 2 for unzip]\n");
@@ -96,6 +101,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
asm_opt->purge_overlap_len);
fprintf(stderr, " --purge-cov INT\n");
fprintf(stderr, " coverage upper bound of Purge-dups [auto]\n");
///fprintf(stderr, " --high-het enable this mode for high heterozygosity sample [experimental, not stable]\n");
fprintf(stderr, " Hi-C-partition [experimental, not stable]:\n");
@@ -157,6 +163,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->recover_atg_cov_min = -1024;
asm_opt->recover_atg_cov_max = INT_MAX;
asm_opt->hom_global_coverage = -1;
asm_opt->hom_global_coverage_set = 0;
asm_opt->bed_inconsist_rate = 70;
asm_opt->hic_inconsist_rate = 30;
///asm_opt->bub_mer_length = 3;
@@ -165,6 +172,8 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->b_high_cov = -1;
asm_opt->m_rate = 0.75;
asm_opt->hap_occ = 1;
asm_opt->polyploidy = 2;
asm_opt->trio_flag_occ_thres = 60;
}
void destory_enzyme(enzyme* f)
@@ -616,7 +625,11 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 306) asm_opt->max_ov_diff_final = atof(opt.arg);
else if (c == 307) asm_opt->extract_list = opt.arg;
else if (c == 308) asm_opt->extract_iter = atoi(opt.arg);
else if (c == 309) asm_opt->hom_global_coverage = atoi(opt.arg);
else if (c == 309)
{
asm_opt->hom_global_coverage = atoi(opt.arg);
asm_opt->hom_global_coverage_set = 1;
}
else if (c == 310)
{
char* s = NULL;
@@ -636,6 +649,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 317) asm_opt->b_low_cov = atoi(opt.arg);
else if (c == 318) asm_opt->b_high_cov = atoi(opt.arg);
else if (c == 319) asm_opt->m_rate = atof(opt.arg);
else if (c == 320) asm_opt->flag |= HA_F_PARTITION;
else if (c == 321) asm_opt->trio_flag_occ_thres = atoi(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);