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Merge branch 'master' into dev-lh3

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This commit is contained in:
Heng Li
2021-03-02 19:27:44 -05:00
parent 205eadf346 d2ca12604b
commit 8e98fb2276
17 changed files with 16486 additions and 4393 deletions
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CommandLines.cpp
+187 -7
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@@ -26,6 +26,12 @@ static ko_longopt_t long_options[] = {
{ "high-het", ko_no_argument, 311 },
{ "lowQ", ko_required_argument, 312 },
{ "min-hist-cnt", ko_required_argument, 313 },
{ "h1", ko_required_argument, 314 },
{ "h2", ko_required_argument, 315 },
{ "enzyme", ko_required_argument, 316 },
{ "b-cov", ko_required_argument, 317 },
{ "h-cov", ko_required_argument, 318 },
{ "m-rate", ko_required_argument, 319 },
{ 0, 0, 0 }
};
@@ -63,6 +69,14 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -u disable post join contigs step which may improve N50\n");
fprintf(stderr, " --lowQ INT\n");
fprintf(stderr, " output contig regions with >=INT%% inconsistency in BED format; 0 to disable [%d]\n", asm_opt->bed_inconsist_rate);
fprintf(stderr, " --b-cov INT\n");
fprintf(stderr, " break contigs at positions with <INT-fold coverage; work with '--m-rate'; 0 to disable [%d]\n", asm_opt->b_low_cov);
fprintf(stderr, " --h-cov INT\n");
fprintf(stderr, " break contigs at positions with >INT-fold coverage; work with '--m-rate'; -1 to disable [%d]\n", asm_opt->b_high_cov);
fprintf(stderr, " --m-rate FLOAT\n");
fprintf(stderr, " break contigs at positions with <=FLOAT*coverage exact overlaps;\n");
fprintf(stderr, " only work with '--b-cov' or '--h-cov'[%.2f]\n", asm_opt->m_rate);
// fprintf(stderr, " --pri-range INT1[,INT2]\n");
// fprintf(stderr, " keep contigs with coverage in this range in p_ctg.gfa; -1 to disable [auto,inf]\n");
@@ -84,6 +98,9 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " coverage upper bound of Purge-dups [auto]\n");
fprintf(stderr, " --high-het enable this mode for high heterozygosity sample [experimental, not stable]\n");
fprintf(stderr, " Hi-C-partition [experimental, not stable]:\n");
fprintf(stderr, " --h1 FILEs file names of Hi-C R1 [r1_1.fq,r1_2.fq,...]\n");
fprintf(stderr, " --h2 FILEs file names of Hi-C R2 [r2_1.fq,r2_2.fq,...]\n");
fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n");
fprintf(stderr, "See `man ./hifiasm.1' for detailed description of these command-line options.\n");
@@ -98,8 +115,12 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->read_file_names = NULL;
asm_opt->output_file_name = (char*)(DEFAULT_OUTPUT);
asm_opt->required_read_name = NULL;
asm_opt->hic_enzymes = NULL;
asm_opt->hic_reads[0] = NULL;
asm_opt->hic_reads[1] = NULL;
asm_opt->thread_num = 1;
asm_opt->k_mer_length = 51;
asm_opt->hic_mer_length = 31;
asm_opt->mz_win = 51;
asm_opt->mz_sample_dist = 500;
asm_opt->bf_shift = 37;
@@ -131,19 +152,42 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->purge_level_primary = 2;
asm_opt->purge_level_trio = 0;
asm_opt->purge_simi_rate = 0.75;
asm_opt->purge_simi_rate_hic = 0.85;
asm_opt->purge_overlap_len = 1;
asm_opt->purge_overlap_len_hic = 50;
asm_opt->recover_atg_cov_min = -1024;
asm_opt->recover_atg_cov_max = INT_MAX;
asm_opt->hom_global_coverage = -1;
asm_opt->bed_inconsist_rate = 70;
asm_opt->hic_inconsist_rate = 30;
///asm_opt->bub_mer_length = 3;
asm_opt->bub_mer_length = 1000000;
asm_opt->b_low_cov = 0;
asm_opt->b_high_cov = -1;
asm_opt->m_rate = 0.75;
}
void destory_enzyme(enzyme* f)
{
int i;
if(f != NULL)
{
for (i = 0; i < f->n; i++)
{
free(f->a[i]);
}
free(f->a);
free(f->l);
free(f);
}
}
void destory_opt(hifiasm_opt_t* asm_opt)
{
if(asm_opt->read_file_names != NULL)
{
free(asm_opt->read_file_names);
}
if(asm_opt->read_file_names != NULL) free(asm_opt->read_file_names);
if(asm_opt->hic_enzymes != NULL) destory_enzyme(asm_opt->hic_enzymes);
if(asm_opt->hic_reads[0] != NULL) destory_enzyme(asm_opt->hic_reads[0]);
if(asm_opt->hic_reads[1] != NULL) destory_enzyme(asm_opt->hic_reads[1]);
}
void ha_opt_reset_to_round(hifiasm_opt_t* asm_opt, int round)
@@ -183,6 +227,16 @@ static int check_file(char* name, const char* opt)
return 1;
}
static int check_hic_reads(enzyme* f, const char* opt)
{
int i;
for (i = 0; i < f->n; i++)
{
if(check_file(f->a[i], opt) == 0) return 0;
}
return 1;
}
int check_option(hifiasm_opt_t* asm_opt)
{
if(asm_opt->read_file_names == NULL || asm_opt->num_reads == 0)
@@ -327,7 +381,7 @@ int check_option(hifiasm_opt_t* asm_opt)
if(asm_opt->bed_inconsist_rate < 0 || asm_opt->bed_inconsist_rate > 100)
{
fprintf(stderr, "[ERROR] inconsistency rate should be [0, 100] (--pb-range)\n");
fprintf(stderr, "[ERROR] inconsistency rate should be [0, 100] (--lowQ)\n");
return 0;
}
@@ -337,6 +391,69 @@ int check_option(hifiasm_opt_t* asm_opt)
if(asm_opt->fn_bin_list[0] != NULL && check_file(asm_opt->fn_bin_list[0], "LIST1") == 0) return 0;
if(asm_opt->fn_bin_list[1] != NULL && check_file(asm_opt->fn_bin_list[1], "LIST2") == 0) return 0;
if(asm_opt->required_read_name != NULL && check_file(asm_opt->required_read_name, "b") == 0) return 0;
if(asm_opt->hic_reads[0] != NULL && check_hic_reads(asm_opt->hic_reads[0], "HIC1") == 0) return 0;
if(asm_opt->hic_reads[1] != NULL && check_hic_reads(asm_opt->hic_reads[1], "HIC2") == 0) return 0;
if(asm_opt->hic_reads[0] != NULL && asm_opt->hic_reads[1] == NULL)
{
fprintf(stderr, "[ERROR] lack r2 of HiC reads (--h2)\n");
return 0;
}
if(asm_opt->hic_reads[1] != NULL && asm_opt->hic_reads[0] == NULL)
{
fprintf(stderr, "[ERROR] lack r1 of HiC reads (--h1)\n");
return 0;
}
if(asm_opt->hic_reads[0] != NULL && asm_opt->hic_reads[1] != NULL &&
asm_opt->hic_reads[0]->n != asm_opt->hic_reads[1]->n)
{
fprintf(stderr, "[ERROR] wrong r1 and r2 of HiC reads (--h1 && --h2)\n");
return 0;
}
if(asm_opt->hic_enzymes != NULL && asm_opt->hic_enzymes->n == 0)
{
fprintf(stderr, "[ERROR] wrong HiC enzymes (--enzyme)\n");
return 0;
}
if(asm_opt->hic_reads[0] != NULL && asm_opt->hic_reads[0]->n == 0)
{
fprintf(stderr, "[ERROR] wrong r1 of HiC reads (--h1)\n");
return 0;
}
if(asm_opt->hic_reads[1] != NULL && asm_opt->hic_reads[1]->n == 0)
{
fprintf(stderr, "[ERROR] wrong r2 of HiC reads (--h2)\n");
return 0;
}
if(asm_opt->b_low_cov < 0)
{
fprintf(stderr, "[ERROR] must >= 0 (--b-cov)\n");
return 0;
}
if(asm_opt->b_high_cov != -1 && asm_opt->b_high_cov < 0)
{
fprintf(stderr, "[ERROR] must >= 0 (--h-cov)\n");
return 0;
}
if(asm_opt->m_rate < 0)
{
fprintf(stderr, "[ERROR] must >= 0 (--m-rate)\n");
return 0;
}
if(asm_opt->b_high_cov != -1 && asm_opt->b_high_cov <= asm_opt->b_low_cov)
{
fprintf(stderr, "[ERROR] [--h-cov] must >= [--b-cov]\n");
return 0;
}
// fprintf(stderr, "input file num: %d\n", asm_opt->num_reads);
// fprintf(stderr, "output file: %s\n", asm_opt->output_file_name);
// fprintf(stderr, "number of threads: %d\n", asm_opt->thread_num);
@@ -386,6 +503,61 @@ void get_queries(int argc, char *argv[], ketopt_t* opt, hifiasm_opt_t* asm_opt)
}
}
void get_hic_enzymes(char *argv, enzyme** x, int check_name)
{
int i, k, pre_i, len = strlen(argv);
(*x) = (enzyme*)calloc(1, sizeof(enzyme));
if(len == 0)
{
(*x)->n = 0; (*x)->l = NULL; (*x)->a = NULL;
return;
}
(*x)->n = 1;
for (i = pre_i = 0; i < len; i++)
{
if(argv[i] == ',')
{
(*x)->n++;
continue;
}
if(check_name)
{
if(argv[i] != 'A' && argv[i] != 'C' && argv[i] != 'G' && argv[i] != 'T' &&
argv[i] != 'a' && argv[i] != 'c' && argv[i] != 'g' && argv[i] != 't' &&
argv[i] != 'N' && argv[i] != 'n')
{
(*x)->n = 0;
(*x)->l = NULL;
(*x)->a = NULL;
return;
}
}
}
(*x)->l = (int*)calloc((*x)->n, sizeof(int));
(*x)->a = (char**)calloc((*x)->n, sizeof(char*));
for (i = pre_i = k = 0; i < len; i++)
{
if(argv[i] == ',')
{
(*x)->l[k] = i - pre_i;
(*x)->a[k] = (char*)malloc(sizeof(char)*((*x)->l[k]+1));
memcpy((*x)->a[k], argv + pre_i, (*x)->l[k]);
(*x)->a[k][(*x)->l[k]] = '\0';
pre_i = i + 1;
k++;
}
}
(*x)->l[k] = i - pre_i;
(*x)->a[k] = (char*)malloc(sizeof(char)*((*x)->l[k]+1));
memcpy((*x)->a[k], argv + pre_i, (*x)->l[k]);
(*x)->a[k][(*x)->l[k]] = '\0';
}
int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
{
@@ -451,7 +623,13 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
}
else if (c == 311) asm_opt->flag |= HA_F_HIGH_HET;
else if (c == 312) asm_opt->bed_inconsist_rate = atoi(opt.arg);
else if (c == 313) asm_opt->min_hist_kmer_cnt = atoi(opt.arg);
else if (c == 313) asm_opt->min_hist_kmer_cnt = atoi(opt.arg);
else if (c == 314) get_hic_enzymes(opt.arg, &(asm_opt->hic_reads[0]), 0);
else if (c == 315) get_hic_enzymes(opt.arg, &(asm_opt->hic_reads[1]), 0);
else if (c == 316) get_hic_enzymes(opt.arg, &(asm_opt->hic_enzymes), 1);
else if (c == 317) asm_opt->b_low_cov = atoi(opt.arg);
else if (c == 318) asm_opt->b_high_cov = atoi(opt.arg);
else if (c == 319) asm_opt->m_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);
@@ -470,7 +648,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
}
}
if (argc == opt.ind)
{
Print_H(asm_opt);
@@ -479,5 +657,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
get_queries(argc, argv, &opt, asm_opt);
return check_option(asm_opt);
}