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bug fixing

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chhylp123
2021-04-16 22:26:28 -04:00
parent f8ee584291
commit efacf8e796
5 changed files with 68 additions and 1070 deletions
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11
CommandLines.cpp
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@@ -23,7 +23,6 @@ static ko_longopt_t long_options[] = {
{ "ex-iter", ko_required_argument, 308 },
{ "purge-cov", ko_required_argument, 309 },
{ "pri-range", ko_required_argument, 310 },
///{ "high-het", ko_no_argument, 311 },
{ "lowQ", ko_required_argument, 312 },
{ "min-hist-cnt", ko_required_argument, 313 },
{ "h1", ko_required_argument, 314 },
@@ -32,7 +31,7 @@ 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 },
{ "primary", ko_no_argument, 320 },
{ "t-occ", ko_required_argument, 321 },
{ "seed", ko_required_argument, 322 },
{ "n-perturb", ko_required_argument, 323 },
@@ -82,6 +81,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " --m-rate FLOAT\n");
fprintf(stderr, " break contigs at positions with <=FLOAT*coverage exact overlaps;\n");
fprintf(stderr, " only work with '--b-cov' or '--h-cov'[%.2f]\n", asm_opt->m_rate);
fprintf(stderr, " --primary output a primary assembly and an alternate assembly\n");
// fprintf(stderr, " --pri-range INT1[,INT2]\n");
// fprintf(stderr, " keep contigs with coverage in this range in p_ctg.gfa; -1 to disable [auto,inf]\n");
@@ -126,7 +126,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
void init_opt(hifiasm_opt_t* asm_opt)
{
memset(asm_opt, 0, sizeof(hifiasm_opt_t));
asm_opt->flag = 0;
///asm_opt->flag = 0;
asm_opt->flag = HA_F_PARTITION;
asm_opt->coverage = -1;
asm_opt->num_reads = 0;
asm_opt->read_file_names = NULL;
@@ -483,7 +484,7 @@ int check_option(hifiasm_opt_t* asm_opt)
fprintf(stderr, "[ERROR] [-s] must >= 0\n");
return 0;
}
return 1;
}
@@ -644,7 +645,7 @@ 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 == 320) asm_opt->flag -= HA_F_PARTITION;
else if (c == 321) asm_opt->trio_flag_occ_thres = atoi(opt.arg);
else if (c == 322) asm_opt->seed = atol(opt.arg);
else if (c == 323) asm_opt->n_perturb = atoi(opt.arg);