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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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Assembly.cpp
+20 -12
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@@ -1023,10 +1023,10 @@ void ha_ec(int64_t round, int num_pround, int des_idx, uint64_t *tot_b, uint64_t
if(round == asm_opt.number_of_round-1 && asm_opt.is_dbg_het_cnt) CALLOC(het_cnt, R_INF.total_reads);
if (r_out) {
write_pt_index(ha_flt_tab, ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name);
write_pt_index(ha_flt_tab, ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name, 0);
if((asm_opt.flag & HA_F_VERBOSE_GFA) && (asm_opt.bin_only == 1)) exit(1);///just for debug
}
if (w_tmp) tmp_pt_pro(&ha_flt_tab, &ha_idx, &R_INF, &scb, &asm_opt, asm_opt.output_file_name, round, asm_opt.number_of_round, 0);
if (w_tmp) tmp_pt_pro(&ha_flt_tab, &ha_idx, &R_INF, &scb, &asm_opt, asm_opt.output_file_name, round, asm_opt.number_of_round, 0, 0);
// Output_corrected_fastq();
@@ -1112,7 +1112,7 @@ void ha_overlap_and_correct(int round)
// fprintf(stderr, "[M::%s::%.3f] ==> chaining\n", __func__, yak_realtime_0()-tt0);
// exit(1);
if (r_out) write_pt_index(ha_flt_tab, ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name);
if (r_out) write_pt_index(ha_flt_tab, ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name, 0);
ha_pt_destroy(ha_idx);
ha_idx = NULL;
@@ -1727,6 +1727,7 @@ void Output_PAF()
fclose(output_file);
fprintf(stderr, "PAF has been written.\n");
exit(1);
}
@@ -1952,12 +1953,12 @@ void ha_overlap_final(void)
asm_opt.het_cov = het_cov;
}
void ha_ec_ff(int renew_idx)
void ha_ec_ff(int renew_idx, int8_t pre_load_idx, uint64_t w_tmp)
{
int hom_cov, het_cov;
ha_flt_tab_hp = ha_idx_hp = NULL;
if(ha_idx && renew_idx) {
if((ha_idx) && (renew_idx) && (!pre_load_idx)) {
ha_pt_destroy(ha_idx); ha_idx = NULL;
}
@@ -1966,6 +1967,8 @@ void ha_ec_ff(int renew_idx)
asm_opt.hom_cov = hom_cov; asm_opt.het_cov = het_cov;
}
if (w_tmp) tmp_pt_pro(&ha_flt_tab, &ha_idx, &R_INF, &scb, &asm_opt, asm_opt.output_file_name, asm_opt.number_of_round, asm_opt.number_of_round, 0, 1);
cal_ov_r(asm_opt.thread_num, R_INF.total_reads, renew_idx);
if(asm_opt.write_pos_idx) {
@@ -2076,7 +2079,7 @@ int ha_assemble(void)
// debug_mc_gg_t(MC_NAME, 0, 0);
// quick_debug_phasing(MC_NAME);
extern void ha_extract_print_list(const All_reads *rs, int n_rounds, const char *o);
int r, r0 = -1, hom_cov = -1, ovlp_loaded = 0; uint64_t tot_b, tot_e;
int r, r0 = -1, hom_cov = -1, ovlp_loaded = 0; uint64_t tot_b, tot_e; int8_t pre_load_ff = 0;
if ((asm_opt.load_index_from_disk) && (asm_opt.dbg_ec_rr < 0) && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf, asm_opt.output_file_name)) {
ovlp_loaded = 1;
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> loaded corrected reads and overlaps from disk\n", __func__, yak_realtime(), yak_cpu_usage());
@@ -2093,13 +2096,13 @@ int ha_assemble(void)
}
if (!ovlp_loaded) {
ha_flt_tab = ha_idx = NULL;
if((asm_opt.flag & HA_F_VERBOSE_GFA)) load_pt_index(&ha_flt_tab, &ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name), load_ct_index(&ha_ct_table, asm_opt.output_file_name);
if((asm_opt.flag & HA_F_VERBOSE_GFA)) load_pt_index(&ha_flt_tab, &ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name, 0), load_ct_index(&ha_ct_table, asm_opt.output_file_name);
r = ha_idx?asm_opt.number_of_round-1:0;
if((!ha_idx) && (asm_opt.restart)) {
r = asm_opt.number_of_round - 1;
r = asm_opt.number_of_round/** - 1**/;
if(asm_opt.dbg_ec_rr >= 0) r = asm_opt.dbg_ec_rr;
for (; r >= 0; --r) {
if(tmp_pt_pro(&ha_flt_tab, &ha_idx, &R_INF, &scb, &asm_opt, asm_opt.output_file_name, r, asm_opt.number_of_round, 1)) {
if(tmp_pt_pro(&ha_flt_tab, &ha_idx, &R_INF, &scb, &asm_opt, asm_opt.output_file_name, r, asm_opt.number_of_round, 1, ((r==asm_opt.number_of_round)?(1):(0)))) {
load_ct_index(&ha_ct_table, asm_opt.output_file_name); r0 = r;
break;
}
@@ -2108,7 +2111,11 @@ int ha_assemble(void)
fprintf(stderr, "[E::%s] no matching debug error-correction bins found\n", __func__);
exit(1);
}
if(r < 0) r = 0;
if(r < 0) {
r = 0;
} else if(r == asm_opt.number_of_round) {
pre_load_ff = 1;
}
}
// construct hash table for high occurrence k-mers
@@ -2138,8 +2145,9 @@ int ha_assemble(void)
// overlap between corrected reads
ha_opt_reset_to_round(&asm_opt, asm_opt.number_of_round);
// ha_overlap_final();
ha_ec_ff(1/**0**/);
ha_ec_ff(1/**0**/, pre_load_ff, ((r > r0) && (asm_opt.restart))?1:0);
fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> found overlaps for the final round\n", __func__, yak_realtime(), yak_cpu_usage(), yak_peakrss_in_gb());
if(asm_opt.dbg_ec_rr >= 0) exit(1);
// fprintf(stderr, "\n[M::%s::%.3f*%.2f@%.3fGB] ==> found overlaps for the final round\n", __func__, yak_realtime(), yak_cpu_usage(), yak_peakrss_in_gb());
// ha_print_ovlp_stat(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads);
if(!(asm_opt.write_pos_idx)) {
@@ -2193,7 +2201,7 @@ int ha_assemble_pair(void)
// Output_corrected_reads(); exit(0);
ha_flt_tab = ha_idx = NULL; r = asm_opt.number_of_round - 1;
if((asm_opt.flag & HA_F_VERBOSE_GFA)) load_pt_index(&ha_flt_tab, &ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name), load_ct_index(&ha_ct_table, asm_opt.output_file_name);
if((asm_opt.flag & HA_F_VERBOSE_GFA)) load_pt_index(&ha_flt_tab, &ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name, 0), load_ct_index(&ha_ct_table, asm_opt.output_file_name);
// construct hash table for high occurrence k-mers
if (!(asm_opt.flag & HA_F_NO_KMER_FLT) && ha_flt_tab == NULL) {