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update for reference read hpc

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chhylp123
2024-10-27 13:22:06 -04:00
parent fc98214321
commit ade800990e
6 changed files with 201 additions and 36 deletions
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6
CommandLines.cpp
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@@ -71,6 +71,7 @@ static ko_longopt_t long_options[] = {
{ "telo-d", ko_required_argument, 356},
{ "telo-s", ko_required_argument, 357},
{ "ctg-n", ko_required_argument, 358},
{ "ont", ko_no_argument, 359},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -91,6 +92,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -t INT number of threads [%d]\n", asm_opt->thread_num);
fprintf(stderr, " -h show help information\n");
fprintf(stderr, " --version show version number\n");
fprintf(stderr, " Preset options:\n");
fprintf(stderr, " --ont assemble Oxford Nanopore reads\n");
fprintf(stderr, " Overlap/Error correction:\n");
fprintf(stderr, " -k INT k-mer length (must be <64) [%d]\n", asm_opt->k_mer_length);
fprintf(stderr, " -w INT minimizer window size [%d]\n", asm_opt->mz_win);
@@ -335,6 +338,8 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->telo_pen = 1;
asm_opt->telo_drop = 2000;
asm_opt->telo_mic_sc = 500;
asm_opt->is_ont = 0;
}
void destory_enzyme(enzyme* f)
@@ -906,6 +911,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 356) asm_opt->telo_drop = atol(opt.arg);
else if (c == 357) asm_opt->telo_mic_sc = atol(opt.arg);
else if (c == 358) asm_opt->max_contig_tip = atol(opt.arg);
else if (c == 359) asm_opt->is_ont = 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);
}