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update k-mer peaks

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chhylp123
2020-07-07 13:20:25 -04:00
parent 2e56ef7db5
commit a25c37ed89
9 changed files with 106 additions and 28 deletions
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45
Assembly.cpp
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@@ -632,7 +632,7 @@ void Output_corrected_reads()
void ha_overlap_and_correct(int round)
{
int i, hom_cov;
int i, hom_cov, het_cov;
ha_ovec_buf_t **b;
ha_ecsave_buf_t *e;
@@ -640,7 +640,7 @@ void ha_overlap_and_correct(int round)
CALLOC(b, asm_opt.thread_num);
for (i = 0; i < asm_opt.thread_num; ++i)
b[i] = ha_ovec_init(0, (round == asm_opt.number_of_round - 1));
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, round == 0? 0 : 1, &R_INF, &hom_cov); // build the index
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, round == 0? 0 : 1, &R_INF, &hom_cov, &het_cov); // build the index
if (round == 0 && ha_flt_tab == 0) // then asm_opt.hom_cov hasn't been updated
ha_opt_update_cov(&asm_opt, hom_cov);
if (asm_opt.required_read_name)
@@ -1141,20 +1141,55 @@ long long readNum, long long rescue_threshold, float cluster_threshold)
fprintf(stderr, "[M::%s] took %0.2fs, revise edges #: %lld\n\n", __func__, Get_T()-startTime, revises);
}
void hap_recalculate_peaks(char* output_file_name)
{
destory_read_bin(&R_INF);
destory_ma_hit_t_alloc(R_INF.paf);
destory_ma_hit_t_alloc(R_INF.reverse_paf);
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.ec", 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);
ha_opt_update_cov(&asm_opt, hom_cov);
}
free(R_INF.read_length);
free(R_INF.name_index);
load_All_reads(&R_INF, gfa_name);
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, 1, &R_INF, &hom_cov, &het_cov); // build the index
asm_opt.hom_cov = hom_cov;
asm_opt.het_cov = het_cov;
ha_pt_destroy(ha_idx);
ha_idx = 0;
destory_read_bin(&R_INF);
free(gfa_name);
load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf, asm_opt.output_file_name);
fprintf(stderr, "M::%s has done.\n", __func__);
}
void ha_overlap_final(void)
{
int i, hom_cov;
int i, hom_cov, het_cov;
ha_ovec_buf_t **b;
CALLOC(b, asm_opt.thread_num);
for (i = 0; i < asm_opt.thread_num; ++i)
b[i] = ha_ovec_init(1, 1);
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, 1, &R_INF, &hom_cov); // build the index
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, 1, &R_INF, &hom_cov, &het_cov); // build the index
kt_for(asm_opt.thread_num, worker_ov_final, b, R_INF.total_reads);
ha_pt_destroy(ha_idx);
ha_idx = 0;
for (i = 0; i < asm_opt.thread_num; ++i)
ha_ovec_destroy(b[i]);
free(b);
asm_opt.hom_cov = hom_cov;
asm_opt.het_cov = het_cov;
}
int ha_assemble(void)
@@ -1172,6 +1207,7 @@ int ha_assemble(void)
///if (!(asm_opt.flag & HA_F_SKIP_TRIOBIN)) ha_triobin(&asm_opt);
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) {
// construct hash table for high occurrence k-mers
@@ -1201,6 +1237,7 @@ int ha_assemble(void)
if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF();
ha_triobin(&asm_opt);
}
if(ovlp_loaded == 2) ovlp_loaded = 0;
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,