xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-15 12:47:57 +08:00
Code Issues Packages Projects Releases Wiki Activity

seperate purgeing and hom peak

Browse Source
This commit is contained in:
chhylp123
2021-07-25 11:23:06 -04:00
parent 6a043540b5
commit b14f894160
6 changed files with 87 additions and 22 deletions
Download Patch File Download Diff File Expand all files Collapse all files

22
CommandLines.cpp
View File

@@ -21,7 +21,7 @@ static ko_longopt_t long_options[] = {
{ "max-od-final", ko_no_argument, 306 },
{ "ex-list", ko_required_argument, 307 },
{ "ex-iter", ko_required_argument, 308 },
{ "purge-cov", ko_required_argument, 309 },
{ "hom-cov", ko_required_argument, 309 },
{ "pri-range", ko_required_argument, 310 },
{ "lowQ", ko_required_argument, 312 },
{ "min-hist-cnt", ko_required_argument, 313 },
@@ -39,6 +39,7 @@ static ko_longopt_t long_options[] = {
{ "n-hap", ko_required_argument, 325 },
{ "n-weight", ko_required_argument, 326 },
{ "l-msjoin", ko_required_argument, 327 },
{ "purge-max", ko_required_argument, 328 },
{ 0, 0, 0 }
};
@@ -55,9 +56,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, "Options:\n");
fprintf(stderr, " Input/Output:\n");
fprintf(stderr, " -o STR prefix of output files [%s]\n", asm_opt->output_file_name);
fprintf(stderr, " -i ignore saved read correction and overlaps\n");
fprintf(stderr, " -t INT number of threads [%d]\n", asm_opt->thread_num);
fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen);
fprintf(stderr, " -h show help information\n");
fprintf(stderr, " --version show version number\n");
fprintf(stderr, " Overlap/Error correction:\n");
fprintf(stderr, " -k INT k-mer length (must be <64) [%d]\n", asm_opt->k_mer_length);
@@ -68,12 +68,16 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -r INT round of correction [%d]\n", asm_opt->number_of_round);
fprintf(stderr, " Assembly:\n");
fprintf(stderr, " -a INT round of assembly cleaning [%d]\n", asm_opt->clean_round);
fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen);
fprintf(stderr, " -m INT pop bubbles of <INT in size in contig graphs [%lld]\n", asm_opt->large_pop_bubble_size);
fprintf(stderr, " -p INT pop bubbles of <INT in size in unitig graphs [%lld]\n", asm_opt->small_pop_bubble_size);
fprintf(stderr, " -n INT remove tip unitigs composed of <=INT reads [%d]\n", asm_opt->max_short_tip);
fprintf(stderr, " -x FLOAT max overlap drop ratio [%.2g]\n", asm_opt->max_drop_rate);
fprintf(stderr, " -y FLOAT min overlap drop ratio [%.2g]\n", asm_opt->min_drop_rate);
fprintf(stderr, " -i ignore saved read correction and overlaps\n");
fprintf(stderr, " -u disable post join contigs step which may improve N50\n");
fprintf(stderr, " --hom-cov INT\n");
fprintf(stderr, " homozygous read coverage [auto]\n");
fprintf(stderr, " --lowQ INT\n");
fprintf(stderr, " output contig regions with >=INT%% inconsistency in BED format; 0 to disable [%d]\n", asm_opt->bed_inconsist_rate);
fprintf(stderr, " --b-cov INT\n");
@@ -105,7 +109,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
asm_opt->purge_simi_rate_l2, asm_opt->purge_simi_rate_l3);
fprintf(stderr, " -O INT min number of overlapped reads for duplicate haplotigs [%d]\n",
asm_opt->purge_overlap_len);
fprintf(stderr, " --purge-cov INT\n");
fprintf(stderr, " --purge-max INT\n");
fprintf(stderr, " coverage upper bound of Purge-dups [auto]\n");
fprintf(stderr, " --n-hap INT\n");
fprintf(stderr, " number of haplotypes [%d]\n", asm_opt->polyploidy);
@@ -183,6 +187,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->recover_atg_cov_max = INT_MAX;
asm_opt->hom_global_coverage = -1;
asm_opt->hom_global_coverage_set = 0;
asm_opt->pur_global_coverage = -1;
asm_opt->bed_inconsist_rate = 70;
asm_opt->hic_inconsist_rate = 30;
///asm_opt->bub_mer_length = 3;
@@ -410,7 +415,13 @@ int check_option(hifiasm_opt_t* asm_opt)
if(asm_opt->hom_global_coverage < 0 && asm_opt->hom_global_coverage != -1)
{
fprintf(stderr, "[ERROR] purge duplication coverage threshold should be >= 0 (--purge-cov)\n");
fprintf(stderr, "[ERROR] homozygous read coverage should be >= 0 (--hom-cov)\n");
return 0;
}
if(asm_opt->pur_global_coverage < 0 && asm_opt->pur_global_coverage != -1)
{
fprintf(stderr, "[ERROR] purge duplication coverage threshold should be >= 0 (--purge-max)\n");
return 0;
}
@@ -663,6 +674,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 325) asm_opt->polyploidy = atoi(opt.arg);
else if (c == 326) asm_opt->n_weight = atoi(opt.arg);
else if (c == 327) asm_opt->misjoin_len = atol(opt.arg);
else if (c == 328) asm_opt->pur_global_coverage = 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);