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

integration/print het sites

Browse Source
This commit is contained in:
chhylp123
2022-01-17 18:29:48 -05:00
parent 7af0d85258
commit 0ce5a7ba5b
18 changed files with 2884 additions and 385 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
CommandLines.cpp
View File

@@ -47,6 +47,8 @@ static ko_longopt_t long_options[] = {
{ "ul", ko_required_argument, 333},
{ "unskew", ko_no_argument, 334},
{ "kpt-rate", ko_required_argument, 335},
{ "ul-rate", ko_required_argument, 336},
{ "dbg-het-cnt", ko_no_argument, 337},
{ 0, 0, 0 }
};
@@ -230,6 +232,8 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->kpt_rate = -1;
asm_opt->infor_cov = 3;
asm_opt->s_hap_cov = 3;
asm_opt->ul_error_rate = 0.15;
asm_opt->is_dbg_het_cnt = 0;
}
void destory_enzyme(enzyme* f)
@@ -745,6 +749,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 333) get_hic_enzymes(opt.arg, &(asm_opt->ar), 0);
else if (c == 334) asm_opt->flag |= HA_F_USKEW;
else if (c == 335) asm_opt->kpt_rate = atof(opt.arg);
else if (c == 336) asm_opt->ul_error_rate = atof(opt.arg);
else if (c == 337) asm_opt->is_dbg_het_cnt = 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);