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Merge branch 'master' of https://github.com/chhylp123/Long_read_assembly

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chhylp123
2020-11-16 01:49:07 -05:00
parent d87314a07e eddb8173da
commit 3a1a3750e9
6 changed files with 26 additions and 17 deletions
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CommandLines.cpp
+9 -8
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@@ -24,10 +24,11 @@ static ko_longopt_t long_options[] = {
{ "purge-cov", ko_required_argument, 309 },
{ "pri-range", ko_required_argument, 310 },
{ "high-het", ko_no_argument, 311 },
{ "lowQ", ko_required_argument, 312 },
{ "h1", ko_required_argument, 313 },
{ "h2", ko_required_argument, 314 },
{ "enzyme", ko_required_argument, 315 },
{ "lowQ", ko_required_argument, 312 },
{ "min-hist-cnt", ko_required_argument, 313 },
{ "h1", ko_required_argument, 314 },
{ "h2", ko_required_argument, 315 },
{ "enzyme", ko_required_argument, 316 },
{ 0, 0, 0 }
};
@@ -114,8 +115,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->hom_cov = 20;
asm_opt->het_cov = -1024;
asm_opt->max_n_chain = 100;
asm_opt->k_mer_min_freq = 3;
asm_opt->k_mer_max_freq = 66;
asm_opt->min_hist_kmer_cnt = 5;
asm_opt->load_index_from_disk = 1;
asm_opt->write_index_to_disk = 1;
asm_opt->number_of_round = 3;
@@ -471,8 +471,9 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
}
else if (c == 311) asm_opt->flag |= HA_F_HIGH_HET;
else if (c == 312) asm_opt->bed_inconsist_rate = atoi(opt.arg);
else if (c == 313) asm_opt->hic_files[0] = opt.arg;
else if (c == 314) asm_opt->hic_files[1] = opt.arg;
else if (c == 313) asm_opt->min_hist_kmer_cnt = atoi(opt.arg);
else if (c == 314) asm_opt->hic_files[0] = opt.arg;
else if (c == 315) asm_opt->hic_files[1] = 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);