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kpt_dup

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chhylp123
2021-11-28 19:35:32 -05:00
parent 26aacdcc2c
commit 763634e1a9
7 changed files with 704 additions and 145 deletions
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3
CommandLines.cpp
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@@ -46,6 +46,7 @@ static ko_longopt_t long_options[] = {
{ "hg-size", ko_required_argument, 332},
{ "ul", ko_required_argument, 333},
{ "unskew", ko_no_argument, 334},
{ "kpt-rate", ko_required_argument, 335},
{ 0, 0, 0 }
};
@@ -226,6 +227,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->dp_min_len = 2000;
asm_opt->dp_e = 0.0025;
asm_opt->hg_size = -1;
asm_opt->kpt_rate = -1;
}
void destory_enzyme(enzyme* f)
@@ -740,6 +742,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 332) asm_opt->hg_size = inter_gsize(opt.arg);
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 == 'l')
{ ///0: disable purge_dup; 1: purge containment; 2: purge overlap
asm_opt->purge_level_primary = asm_opt->purge_level_trio = atoi(opt.arg);