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unsucessful hpc mark

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chhylp123
2026-05-15 19:02:16 -04:00
parent 7884b5ad88
commit bca2394b69
12 changed files with 2679 additions and 216 deletions
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CommandLines.cpp
+127 -3
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@@ -12,6 +12,11 @@
KSEQ_INIT(gzFile, gzread)
#define DEFAULT_OUTPUT "hifiasm.asm"
#define RER_H_HiFi 0.06
#define RER_H_ONT 0.08
#define RER_N_HiFi 0.03
#define RER_N_ONT 0.05
#define MIN_R_COV 3
hifiasm_opt_t asm_opt;
@@ -94,7 +99,14 @@ static ko_longopt_t long_options[] = {
{ "hyb-syn", ko_required_argument, 376},
{ "simd-m", ko_required_argument, 377},
{ "del-hf", ko_no_argument, 378},
{ "dbg-rr", ko_required_argument, 379},
{ "dbg-rr", ko_required_argument, 379},///start from 0/1/2 step of correction
{ "re-aln", ko_required_argument, 380},
{ "syn", ko_required_argument, 381},
{ "rec", ko_required_argument, 382},
{ "ref", ko_required_argument, 383},
{ "h_rec", ko_required_argument, 384},
{ "h_ref", ko_required_argument, 385},
{ "ret", ko_no_argument, 386},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -106,6 +118,7 @@ double Get_T(void)
return t.tv_sec+t.tv_usec/1000000.0;
}
void Print_H(hifiasm_opt_t* asm_opt)
{
fprintf(stderr, "Usage: hifiasm [options] <in_1.fq> <in_2.fq> <...>\n");
@@ -140,7 +153,34 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " discard overlaps supported by <INT minimizers [%ld]\n", asm_opt->chn_occ);
fprintf(stderr, " --ec-only error correction only; disable overlapping and assembly\n");
fprintf(stderr, " --simd-m use SIMD acceleration when supported: AVX-512 (2), AVX2 (1), or non-SIMD (0)\n");
fprintf(stderr, " --re-aln keep raw reads for error correction [%d]\n", asm_opt->realn_raw);
fprintf(stderr, " --syn rescue overlaps for error correction [%d]\n", asm_opt->post_syn);
fprintf(stderr, " Recurrent sequencing-error filtering:\n");
fprintf(stderr, " --ret enable recurrent sequencing-error filtering; disabled by default\n");
fprintf(stderr, " thresholds are controlled by --rec/--ref and --h_rec/--h_ref\n");
fprintf(stderr, " --rec/--ref and --h_rec/--h_ref are ignored unless --ret is set\n");
fprintf(stderr, " --rec INT\n");
fprintf(stderr, " discard candidate variants supported by <INT reads [%ld]\n",
asm_opt->recurrent_err_normal_min);
fprintf(stderr, " --ref FLOAT\n");
fprintf(stderr, " discard candidate variants supported by <FLOAT*coverage reads; -1 to disable\n");
fprintf(stderr, " coverage = min(local read coverage, homozygous coverage);\n");
fprintf(stderr, " default: %.3g for ONT, %.3g for HiFi\n",
RER_N_ONT, RER_N_HiFi);
fprintf(stderr, " --h_rec INT\n");
fprintf(stderr, " discard candidate variants near homopolymers if supported by <INT reads [%ld]\n",
asm_opt->recurrent_err_hpc_min);
fprintf(stderr, " --h_ref FLOAT\n");
fprintf(stderr, " discard candidate variants near homopolymers if supported by <FLOAT*coverage reads; -1 to disable\n");
fprintf(stderr, " coverage = min(local read coverage, homozygous coverage);\n");
fprintf(stderr, " default: %.3g for ONT, %.3g for HiFi\n",
RER_H_ONT, RER_H_HiFi);
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);
@@ -365,8 +405,8 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->dp_e = 0.0025;
asm_opt->hg_size = -1;
asm_opt->kpt_rate = -1;
asm_opt->infor_cov = 3;
asm_opt->s_hap_cov = 3;
asm_opt->infor_cov = MIN_R_COV;
asm_opt->s_hap_cov = MIN_R_COV;
asm_opt->ul_error_rate = 0.2/**0.15**/;
asm_opt->ul_error_rate_low = 0.1;
asm_opt->ul_error_rate_hpc = 0.2;
@@ -447,6 +487,22 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->del_hf = 0;
asm_opt->dbg_ec_rr = -1;
asm_opt->realn_raw = 0;
asm_opt->post_syn = 1;
asm_opt->recurrent_err_normal_min = MIN_R_COV;
asm_opt->recurrent_err_normal_min_set = -1;
asm_opt->recurrent_err_normal_rat = RER_N_HiFi;
asm_opt->recurrent_err_normal_rat_set = -1;
asm_opt->recurrent_err_hpc_min = MIN_R_COV;
asm_opt->recurrent_err_hpc_min_set = -1;
asm_opt->recurrent_err_hpc_rat = RER_H_HiFi;
asm_opt->recurrent_err_hpc_rat_set = -1;
asm_opt->recurrent_err_test = 0;
}
void destory_enzyme(enzyme* f)
@@ -837,6 +893,26 @@ int check_option(hifiasm_opt_t* asm_opt)
return 0;
}
if((asm_opt->realn_raw != 0) && (asm_opt->realn_raw != 1)) {
fprintf(stderr, "[ERROR] [--re-aln] must be 0/1\n");
return 0;
}
if((asm_opt->post_syn != 0) && (asm_opt->post_syn != 1)) {
fprintf(stderr, "[ERROR] [--syn] must be 0/1\n");
return 0;
}
if(asm_opt->recurrent_err_normal_rat > 1.0) {
fprintf(stderr, "[ERROR] [--ref] must be >= 0 && <= 1.0; -1 to disable\n");
return 0;
}
if(asm_opt->recurrent_err_hpc_rat > 1.0) {
fprintf(stderr, "[ERROR] [--h_ref] must be >= 0 && <= 1.0; -1 to disable\n");
return 0;
}
return 1;
}
@@ -1126,6 +1202,24 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
asm_opt->del_hf = 1;
} else if (c == 379) {
asm_opt->dbg_ec_rr = atoi(opt.arg);
} else if (c == 380) {
asm_opt->realn_raw = atoi(opt.arg);
} else if (c == 381) {
asm_opt->post_syn = atoi(opt.arg);
} else if (c == 382) {
asm_opt->recurrent_err_normal_min = atoi(opt.arg);
asm_opt->recurrent_err_normal_min_set = 1;
} else if (c == 383) {
asm_opt->recurrent_err_normal_rat = atof(opt.arg);
asm_opt->recurrent_err_normal_rat_set = 1;
} else if (c == 384) {
asm_opt->recurrent_err_hpc_min = atoi(opt.arg);
asm_opt->recurrent_err_hpc_min_set = 1;
} else if (c == 385) {
asm_opt->recurrent_err_hpc_rat = atof(opt.arg);
asm_opt->recurrent_err_hpc_rat_set = 1;
} else if (c == 386) {
asm_opt->recurrent_err_test = 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);
}
@@ -1167,5 +1261,35 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
asm_opt->rl_cut = -1; asm_opt->sc_cut = 1;
}
if(asm_opt->recurrent_err_normal_min_set != 1) {
asm_opt->recurrent_err_normal_min = MIN_R_COV;
}
if(asm_opt->recurrent_err_normal_rat_set != 1) {
asm_opt->recurrent_err_normal_rat = ((asm_opt->is_ont)?(RER_N_ONT):(RER_N_HiFi));
}
if(asm_opt->recurrent_err_hpc_min_set != 1) {
asm_opt->recurrent_err_hpc_min = MIN_R_COV;
}
if(asm_opt->recurrent_err_hpc_rat_set != 1) {
asm_opt->recurrent_err_hpc_rat = ((asm_opt->is_ont)?(RER_H_ONT):(RER_H_HiFi));
}
if(asm_opt->recurrent_err_normal_min < 0) asm_opt->recurrent_err_normal_min = -1;
if(asm_opt->recurrent_err_normal_rat < 0) asm_opt->recurrent_err_normal_rat = -1;
if(asm_opt->recurrent_err_hpc_min < 0) asm_opt->recurrent_err_hpc_min = -1;
if(asm_opt->recurrent_err_hpc_rat < 0) asm_opt->recurrent_err_hpc_rat = -1;
if(asm_opt->recurrent_err_test == 0) {
asm_opt->recurrent_err_normal_min = -1;
asm_opt->recurrent_err_normal_min_set = -1;
asm_opt->recurrent_err_normal_rat = -1;
asm_opt->recurrent_err_normal_rat_set = -1;
asm_opt->recurrent_err_hpc_min = -1;
asm_opt->recurrent_err_hpc_min_set = -1;
asm_opt->recurrent_err_hpc_rat = -1;
asm_opt->recurrent_err_hpc_rat_set = -1;
}
return check_option(asm_opt);
}