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add scaffolding

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chhylp123
2023-10-10 12:40:29 -04:00
parent c7685e6f19
commit 281ae6ba89
7 changed files with 2312 additions and 147 deletions
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14
CommandLines.cpp
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@@ -62,6 +62,8 @@ static ko_longopt_t long_options[] = {
{ "path-min", ko_required_argument, 347},
{ "trio-dual", ko_no_argument, 348},
{ "ul-cut", ko_required_argument, 349},
{ "dual-scaf", ko_no_argument, 350},
{ "scaf-gap", ko_required_argument, 351},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -163,7 +165,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " --l-msjoin INT\n");
fprintf(stderr, " detect misjoined unitigs of >=INT in size; 0 to disable [%lu]\n", asm_opt->misjoin_len);
fprintf(stderr, " Ultra-Long-integration (beta):\n");
fprintf(stderr, " Ultra-Long-integration:\n");
fprintf(stderr, " --ul FILEs file names of Ultra-Long reads [r1.fq,r2.fq,...]\n");
fprintf(stderr, " --ul-rate FLOAT\n");
fprintf(stderr, " error rate of Ultra-Long reads [%.3g]\n", asm_opt->ul_error_rate);
@@ -179,6 +181,11 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " filter out <INT UL reads during the UL assembly [%d]\n", asm_opt->ul_min_base);
// fprintf(stderr, " --low-het enable it for genomes with very low het heterozygosity rate (<0.0001%%)\n");
fprintf(stderr, " Dual-Scaffolding:\n");
fprintf(stderr, " --dual-scaf output scaffolding\n");
fprintf(stderr, " --scaf-gap INT\n");
fprintf(stderr, " max gap size for scaffolding [%ld]\n", asm_opt->self_scaf_gap_max);
fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n");
fprintf(stderr, "See `https://hifiasm.readthedocs.io/en/latest/' or `man ./hifiasm.1' for complete documentation.\n");
}
@@ -295,6 +302,9 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->trio_cov_het_ovlp = -1;
asm_opt->ul_min_base = 0;
asm_opt->self_scaf = 0;
asm_opt->self_scaf_min = 250000;
asm_opt->self_scaf_reliable_min = 5000000;
asm_opt->self_scaf_gap_max = 3000000;
}
void destory_enzyme(enzyme* f)
@@ -841,6 +851,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
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 == 349) asm_opt->ul_min_base = atol(opt.arg);
else if (c == 350) asm_opt->self_scaf = 1;
else if (c == 351) asm_opt->self_scaf_gap_max = atol(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);
}