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fall back to avx2

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chhylp123
2026-04-01 22:28:54 -04:00
parent a137a6b06f
commit 815d709fb9
16 changed files with 1122 additions and 390 deletions
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CommandLines.cpp
+13 -3
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@@ -92,6 +92,7 @@ static ko_longopt_t long_options[] = {
{ "dbg-in2", ko_required_argument, 374},
{ "ec-only", ko_no_argument, 375},
{ "hyb-syn", ko_required_argument, 376},
{ "simd-m", ko_required_argument, 377},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -136,6 +137,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
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, " --simd-m use SIMD acceleration when supported: AVX-512 (2), AVX2 (1), or non-SIMD (0)\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);
@@ -247,7 +250,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " --ont assemble ONT Simplex reads in fastq format\n");
// fprintf(stderr, " --sc-n consider base qual value for assembly\n");
fprintf(stderr, " --chem-c INT\n");
fprintf(stderr, " detect chimeric reads with <=INT other reads support [%lu]\n", asm_opt->chemical_cov);
// fprintf(stderr, " detect chimeric reads with <=INT other reads support [%lu]\n", asm_opt->chemical_cov);
fprintf(stderr, " detect chimeric reads with <=INT other reads support [auto]\n");
fprintf(stderr, " --chem-f INT\n");
fprintf(stderr, " length of flanking regions for chimeric read detection [%lu]\n", asm_opt->chemical_flank);
fprintf(stderr, " --rl-cut INT\n");
@@ -396,7 +400,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->is_ont = 0;
asm_opt->is_sc = 0;
asm_opt->chemical_cov = 1;
asm_opt->chemical_cov = -1/**1**/;
asm_opt->chemical_flank = 256;
asm_opt->ul_mod = 0;
@@ -416,7 +420,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->hf_cutoff = -1;
asm_opt->write_pos_idx = 1;
asm_opt->write_pos_idx = 0/**1**/;
asm_opt->hom_cov_0 = -1;
asm_opt->het_cov_0 = -1;
@@ -433,6 +437,10 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->ec_only = 0;
asm_opt->hyb_syn = 1;
asm_opt->step_rd = -1/**128**/;
asm_opt->dbg_bam = 0/**1**/;
asm_opt->simd_mm = -1;
}
void destory_enzyme(enzyme* f)
@@ -1106,6 +1114,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
asm_opt->ec_only = 1;
} else if (c == 376) {
asm_opt->hyb_syn = atoi(opt.arg);
} else if (c == 377) {
asm_opt->simd_mm = 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);
}