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err_estimate

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chhylp123
2026-03-01 08:51:53 -05:00
parent 2fa4ef224f
commit c0478830e6
7 changed files with 1289 additions and 253 deletions
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CommandLines.cpp
+23 -1
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@@ -90,6 +90,8 @@ static ko_longopt_t long_options[] = {
{ "chn-occ", ko_required_argument, 372},
{ "dbg-in1", ko_required_argument, 373},
{ "dbg-in2", ko_required_argument, 374},
{ "ec-only", ko_no_argument, 375},
{ "hyb-syn", ko_required_argument, 376},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -133,6 +135,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " homozygous read coverage [auto]; used for error correction and assembly; manual value overrides auto\n");
fprintf(stderr, " --chn-occ INT\n");
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, " 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);
@@ -251,7 +254,13 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " filter out ONT Simplex reads shorter than <INT> for assembly [%ld]\n", asm_opt->rl_cut);
fprintf(stderr, " --sc-cut INT\n");
fprintf(stderr, " filter out ONT Simplex reads with a mean base quality score below <INT> [%ld]\n", asm_opt->sc_cut);
fprintf(stderr, " --hf FILEs file names of HiFi reads\n");
fprintf(stderr, " --hf FILEs HiFi read file(s)\n");
fprintf(stderr, " --hyb-syn INT\n");
fprintf(stderr, " hybrid correction mode (requires --hf) [%d]:\n", asm_opt->hyb_syn);
fprintf(stderr, " 1: all-vs-all (ONT<-all, HiFi<-all)\n");
fprintf(stderr, " 2: ONT<-all, HiFi<-HiFi\n");
fprintf(stderr, " 3: mode 2 + ONT/HiFi sync to reduce bias\n");
fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n");
@@ -420,6 +429,10 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->dbg_run_1 = NULL;
asm_opt->dbg_run_2 = NULL;
asm_opt->ec_only = 0;
asm_opt->hyb_syn = 1;
asm_opt->step_rd = 128;
}
void destory_enzyme(enzyme* f)
@@ -805,6 +818,11 @@ int check_option(hifiasm_opt_t* asm_opt)
return 0;
}
if((asm_opt->hyb_syn != 1) && (asm_opt->hyb_syn != 2) && (asm_opt->hyb_syn != 3)) {
fprintf(stderr, "[ERROR] [--hyb-syn] must be 1/2/3\n");
return 0;
}
return 1;
}
@@ -1084,6 +1102,10 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
asm_opt->dbg_run_1 = opt.arg;
} else if (c == 374) {
asm_opt->dbg_run_2 = opt.arg;
} else if (c == 375) {
asm_opt->ec_only = 1;
} else if (c == 376) {
asm_opt->hyb_syn = atoi(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);
}