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fix bug for gen_contain_consensus_chain

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chhylp123
2023-10-22 13:23:27 -04:00
parent 281ae6ba89
commit 4ca8951f9d
12 changed files with 281 additions and 54 deletions
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106
Assembly.cpp
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@@ -649,13 +649,6 @@ static void worker_ovec_cal0(void *data, long i, int tid)
{
ha_ovec_buf_t *b = ((ha_ovec_buf_t**)data)[tid];
int fully_cov, abnormal;
// if(i != 33) return;
// fprintf(stderr, "[M::%s-beg] rid->%ld\n", __func__, i);
// if (memcmp("m64012_190920_173625/88015004/ccs", Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
// fprintf(stderr, "[M::%s-beg] rid->%ld\n", __func__, i);
// } else {
// return;
// }
ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist,
0.02, asm_opt.max_n_chain, 1, NULL/**&(b->k_flag)**/, &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region), NULL, &(b->sp));
@@ -664,17 +657,24 @@ static void worker_ovec_cal0(void *data, long i, int tid)
clear_Round2_alignment(&b->round2);
correct_overlap(&b->olist, &R_INF, &b->self_read, &b->correct, &b->ovlp_read, &b->POA_Graph, &b->DAGCon,
&b->cigar1, &b->hap, &b->round2, &b->r_buf, &(b->tmp_region.w_list), 0, 0, &fully_cov, &abnormal);
&b->cigar1, &b->hap, &b->round2, &b->r_buf, &(b->tmp_region.w_list), 0, 0/**1***/, &fully_cov, &abnormal);
b->num_read_base += b->self_read.length;
b->num_correct_base += b->correct.corrected_base;
b->num_recorrect_base += b->round2.dumy.corrected_base;
R_INF.paf[i].is_fully_corrected = 0;
R_INF.paf[i].is_abnormal = abnormal;
// R_INF.paf[i].is_fully_corrected = 0;
// R_INF.paf[i].is_abnormal = abnormal;
R_INF.trio_flag[i] = AMBIGU;
// R_INF.paf[i].is_fully_corrected = 0;
// if (fully_cov) {
// if (get_cigar_errors(&b->cigar1) == 0 && get_cigar_errors(&b->round2.cigar) == 0)
// R_INF.paf[i].is_fully_corrected = 1;
// }
// R_INF.paf[i].is_abnormal = abnormal;
// R_INF.trio_flag[i] = AMBIGU;
push_final_overlaps(&(R_INF.paf[i]), R_INF.reverse_paf, &b->olist, 1);
push_final_overlaps(&(R_INF.reverse_paf[i]), R_INF.reverse_paf, &b->olist, 2);
@@ -920,7 +920,7 @@ void rescue_hp_reads(ha_ovec_buf_t **b)
int hom_cov, het_cov;
ha_flt_tab_hp = ha_idx_hp = NULL;
if (!(asm_opt.flag & HA_F_NO_KMER_FLT)) {
ha_flt_tab_hp = ha_ft_gen(&asm_opt, &R_INF, &hom_cov, 1);
ha_flt_tab_hp = ha_ft_gen(&asm_opt, &R_INF, &hom_cov, 1, 0);
}
ha_idx_hp = ha_pt_gen(&asm_opt, ha_flt_tab, 1, 1, &R_INF, &hom_cov, &het_cov);
@@ -1038,7 +1038,7 @@ void ha_overlap_and_correct(int round)
///debug_print_pob_regions();
}
void ha_overlap_cal(int round)
void ha_overlap_cal(int round, int read_from_store)
{
int i, hom_cov, het_cov;
ha_ovec_buf_t **b;
@@ -1049,9 +1049,9 @@ void ha_overlap_cal(int round)
for (i = 0; i < asm_opt.thread_num; ++i)
b[i] = ha_ovec_init(0, (round == asm_opt.number_of_round - 1),0);
if(ha_idx) hom_cov = asm_opt.hom_cov;
if(ha_idx == NULL) ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, round == 0? 0 : 1, 0, &R_INF, &hom_cov, &het_cov); // build the index
if(ha_idx == NULL) ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, ((round == 0)&&(read_from_store == 0))?0:1, 0, &R_INF, &hom_cov, &het_cov); // build the index
///debug_adapter(&asm_opt, &R_INF);
if (round == 0 && ha_flt_tab == 0) // then asm_opt.hom_cov hasn't been updated
if (/**round == 0 &&**/ ha_flt_tab == 0) // then asm_opt.hom_cov hasn't been updated
ha_opt_update_cov(&asm_opt, hom_cov);
het_cnt = NULL;
if(round == asm_opt.number_of_round-1 && asm_opt.is_dbg_het_cnt) CALLOC(het_cnt, R_INF.total_reads);
@@ -1075,6 +1075,8 @@ void ha_overlap_cal(int round)
ha_ovec_destroy(b[i]);
}
free(b);
asm_opt.hom_cov = hom_cov;
asm_opt.het_cov = het_cov;
}
@@ -1787,7 +1789,7 @@ void hap_recalculate_peaks(char* output_file_name)
int hom_cov, het_cov;
// construct hash table for high occurrence k-mers
if (!(asm_opt.flag & HA_F_NO_KMER_FLT)) {
ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF, &hom_cov, 0);
ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF, &hom_cov, 0, 0);
ha_opt_update_cov(&asm_opt, hom_cov);
}
free(R_INF.read_length);
@@ -1898,13 +1900,13 @@ int ha_assemble_ovec(void)
// construct hash table for high occurrence k-mers
if (!(asm_opt.flag & HA_F_NO_KMER_FLT) && ha_flt_tab == NULL)
{
ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF, &hom_cov, 0);
ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF, &hom_cov, 0, 0);
ha_opt_update_cov(&asm_opt, hom_cov);
}
// error correction
assert(asm_opt.number_of_round > 0);
ha_opt_reset_to_round(&asm_opt, r); // this update asm_opt.roundID and a few other fields
ha_overlap_cal(r);
ha_overlap_cal(r, 0);
fprintf(stderr, "[M::%s] size of buffer: %.3fGB\n", __func__, asm_opt.mem_buf / 1073741824.0);
@@ -1944,7 +1946,7 @@ int ha_assemble(void)
// construct hash table for high occurrence k-mers
if (!(asm_opt.flag & HA_F_NO_KMER_FLT) && ha_flt_tab == NULL)
{
ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF, &hom_cov, 0);
ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF, &hom_cov, 0, 0);
ha_opt_update_cov(&asm_opt, hom_cov);
}
// error correction
@@ -1978,3 +1980,69 @@ int ha_assemble(void)
destory_All_reads(&R_INF);
return 0;
}
int ha_assemble_pair(void)
{
extern void ha_extract_print_list(const All_reads *rs, int n_rounds, const char *o);
int r = 0, hom_cov = -1, ovlp_loaded = 0; memset((&R_INF), 0, sizeof(R_INF));
if (asm_opt.load_index_from_disk && 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());
if (asm_opt.extract_list) {
ha_extract_print_list(&R_INF, asm_opt.extract_iter, asm_opt.extract_list);
exit(0);
}
if (asm_opt.flag & HA_F_WRITE_EC) Output_corrected_reads();
if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF();
if (asm_opt.het_cov == -1024) hap_recalculate_peaks(asm_opt.output_file_name), ovlp_loaded = 2;
}
if (!ovlp_loaded) {
if(!append_All_reads(&R_INF, asm_opt.output_file_name, 0)) {
fprintf(stderr, "[M::%s::] Cannot load %s.0\n", __func__, asm_opt.output_file_name);
exit(1);
}
if(!append_All_reads(&R_INF, asm_opt.output_file_name, 1)) {
fprintf(stderr, "[M::%s::] Cannot load %s.1\n", __func__, asm_opt.output_file_name);
exit(1);
}
// 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);
// construct hash table for high occurrence k-mers
if (!(asm_opt.flag & HA_F_NO_KMER_FLT) && ha_flt_tab == NULL) {
ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF, &hom_cov, 0, 1);
ha_opt_update_cov(&asm_opt, hom_cov);
}
// error correction
assert(asm_opt.number_of_round > 0);
ha_opt_reset_to_round(&asm_opt, r); // this update asm_opt.roundID and a few other fields
ha_overlap_cal(r, 1);
fprintf(stderr, "[M::%s] size of buffer: %.3fGB\n", __func__, asm_opt.mem_buf / 1073741824.0);
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.flag & HA_F_WRITE_EC) Output_corrected_reads();
ha_print_ovlp_stat(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads);
ha_ft_destroy(ha_flt_tab);
if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF();
ha_triobin(&asm_opt);
}
if(ovlp_loaded == 2) ovlp_loaded = 0;
ha_opt_update_cov_min(&asm_opt, asm_opt.hom_cov, MIN_N_CHAIN);
build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf,
R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round,
asm_opt.gap_fuzz, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name, asm_opt.large_pop_bubble_size, 0, !ovlp_loaded);
destory_All_reads(&R_INF);
return 0;
}