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0.16.0 release

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chhylp123
2021-08-22 21:58:00 -04:00
parent 37b07e4d33
commit e230b3a55f
10 changed files with 126 additions and 85 deletions
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CommandLines.cpp
+36 -1
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@@ -43,6 +43,7 @@ static ko_longopt_t long_options[] = {
{ "fast", ko_no_argument, 329 },
{ "dp-er", ko_required_argument, 330},
{ "max-kocc", ko_required_argument, 331},
{ "hg-size", ko_required_argument, 332},
{ 0, 0, 0 }
};
@@ -70,6 +71,10 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -N INT consider up to max(-D*coverage,-N) overlaps for each oriented read [%d]\n", asm_opt->max_n_chain);
fprintf(stderr, " -r INT round of correction [%d]\n", asm_opt->number_of_round);
fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen);
fprintf(stderr, " --max-kocc INT\n");
fprintf(stderr, " employ k-mers occurring <INT times to rescue repetitive overlaps [%d]\n", asm_opt->max_kmer_cnt);
fprintf(stderr, " --hg-size INT(k, m or g)\n");
fprintf(stderr, " estimated haploid genome size used for inferring read coverage [auto]\n");
fprintf(stderr, " Assembly:\n");
fprintf(stderr, " -a INT round of assembly cleaning [%d]\n", asm_opt->clean_round);
fprintf(stderr, " -m INT pop bubbles of <INT in size in contig graphs [%lld]\n", asm_opt->large_pop_bubble_size);
@@ -213,6 +218,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->scffold = 0;
asm_opt->dp_min_len = 2000;
asm_opt->dp_e = 0.0025;
asm_opt->hg_size = -1;
}
void destory_enzyme(enzyme* f)
@@ -514,6 +520,18 @@ int check_option(hifiasm_opt_t* asm_opt)
return 0;
}
if(asm_opt->max_kmer_cnt < 0)
{
fprintf(stderr, "[ERROR] [--max-kocc] must >= 0\n");
return 0;
}
if(asm_opt->hg_size < -1)
{
fprintf(stderr, "[ERROR] [--hg-size] wrong genome size\n");
return 0;
}
return 1;
}
@@ -599,6 +617,23 @@ void get_hic_enzymes(char *argv, enzyme** x, int check_name)
(*x)->a[k][(*x)->l[k]] = '\0';
}
int64_t inter_gsize(char *argv)
{
int64_t len = strlen(argv);
double s;
if(len <= 1) return -2;
char t = argv[len-1];
if(t != 'k' && t != 'K' && t != 'm' && t != 'M' && t != 'g' && t != 'G') return -2;
char *ss=(char*)malloc(len);
memcpy(ss, argv, len-1); ss[len-1] = '\0';
s = atof(ss);
free(ss);
if(t == 'k' || t == 'K') return s*1000;
if(t == 'm' || t == 'M') return s*1000000;
if(t == 'g' || t == 'G') return s*1000000000;
return s;
}
int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
{
ketopt_t opt = KETOPT_INIT;
@@ -686,6 +721,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 329) asm_opt->flag |= HA_F_FAST;
else if (c == 330) asm_opt->dp_e = atof(opt.arg);
else if (c == 331) asm_opt->max_kmer_cnt = atol(opt.arg);
else if (c == 332) asm_opt->hg_size = inter_gsize(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);
@@ -716,6 +752,5 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
get_queries(argc, argv, &opt, asm_opt);
return check_option(asm_opt);
}