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

fix bug for gen_contain_consensus_chain

Browse Source
This commit is contained in:
chhylp123
2023-10-22 13:23:27 -04:00
parent 281ae6ba89
commit 4ca8951f9d
12 changed files with 281 additions and 54 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
CommandLines.cpp
View File

@@ -64,6 +64,7 @@ static ko_longopt_t long_options[] = {
{ "ul-cut", ko_required_argument, 349},
{ "dual-scaf", ko_no_argument, 350},
{ "scaf-gap", ko_required_argument, 351},
{ "sec-in", ko_required_argument, 352},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -305,6 +306,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->self_scaf_min = 250000;
asm_opt->self_scaf_reliable_min = 5000000;
asm_opt->self_scaf_gap_max = 3000000;
asm_opt->sec_in = NULL;
}
void destory_enzyme(enzyme* f)
@@ -853,6 +855,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
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 == 352) get_hic_enzymes(opt.arg, &(asm_opt->sec_in), 0);
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);
}