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fixed het/hom node bugs

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chhylp123
2022-12-08 03:07:14 -05:00
parent a3b72457f0
commit a674110b23
6 changed files with 67 additions and 21 deletions
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12
CommandLines.cpp
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@@ -49,6 +49,8 @@ static ko_longopt_t long_options[] = {
{ "kpt-rate", ko_required_argument, 335},
{ "ul-rate", ko_required_argument, 336},
{ "dbg-het-cnt", ko_no_argument, 337},
{ "ul-tip", ko_required_argument, 338},
{ "low-het", ko_no_argument, 339},
{ 0, 0, 0 }
};
@@ -146,8 +148,10 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " Ultra-Long-integration (beta):\n");
fprintf(stderr, " --ul FILEs file names of Ultra-Long reads [r1.fq,r2.fq,...]\n");
fprintf(stderr, " --ul-rate FLOAT\n");
fprintf(stderr, " similarity threshold for UL-to-HiFi alignment [%.3g]\n", asm_opt->ul_error_rate);
fprintf(stderr, " error rate of Ultra-Long reads [%.3g]\n", asm_opt->ul_error_rate);
fprintf(stderr, " --ul-tip INT\n");
fprintf(stderr, " remove tip unitigs composed of <=INT reads for the UL assembly [%d]\n", asm_opt->max_short_ul_tip);
// fprintf(stderr, " --low-het enable it for genomes with very low het heterozygosity rate (<0.0001%%)\n");
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");
@@ -204,6 +208,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->min_overlap_Len = 50;
asm_opt->min_overlap_coverage = 0;
asm_opt->max_short_tip = 3;
asm_opt->max_short_ul_tip = 6;
asm_opt->min_cnt = 2;
asm_opt->mid_cnt = 5;
asm_opt->purge_level_primary = 3;
@@ -246,6 +251,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->ul_error_rate_hpc = 0.2;
asm_opt->ul_ec_round = 3;
asm_opt->is_dbg_het_cnt = 0;
asm_opt->is_low_het_ul = 0;
}
void destory_enzyme(enzyme* f)
@@ -763,6 +769,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
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 == 338) asm_opt->max_short_ul_tip = atol(opt.arg);
else if (c == 339) asm_opt->is_low_het_ul = 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);