mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-25 22:08:12 +08:00
for high-het and coverage
This commit is contained in:
chhylp123
+290
-40
@@ -9384,13 +9384,19 @@ ma_hit_t_alloc* sources, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp)
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uint32_t get_ug_coverage(ma_utg_t* u, asg_t* read_g, const ma_sub_t* coverage_cut,
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ma_hit_t_alloc* sources, R_to_U* ruIndex)
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ma_hit_t_alloc* sources, R_to_U* ruIndex, uint8_t* r_flag)
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{
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uint32_t k, j, rId, tn, is_Unitig;
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long long R_bases = 0, C_bases = 0;
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ma_hit_t *h;
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if(u->m == 0) return 0;
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for (k = 0; k < u->n; k++)
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{
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rId = u->a[k]>>33;
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r_flag[rId] = 1;
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}
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for (k = 0; k < u->n; k++)
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{
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rId = u->a[k]>>33;
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@@ -9407,16 +9413,25 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex)
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if(tn == (uint32_t)-1 || is_Unitig == 1 || read_g->seq[tn].del == 1) continue;
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}
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if(read_g->seq[tn].del == 1) continue;
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if(r_flag[tn] != 1) continue;
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C_bases += (Get_qe((*h)) - Get_qs((*h)));
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}
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}
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for (k = 0; k < u->n; k++)
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{
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rId = u->a[k]>>33;
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r_flag[rId] = 0;
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}
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return C_bases/R_bases;
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}
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void ma_ug_print2(const ma_ug_t *ug, All_reads *RNF, asg_t* read_g, const ma_sub_t *coverage_cut,
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ma_hit_t_alloc* sources, R_to_U* ruIndex, int print_seq, const char* prefix, FILE *fp)
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{
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uint8_t* primary_flag = (uint8_t*)calloc(read_g->n_seq, sizeof(uint8_t));
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uint32_t i, j, l;
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char name[32];
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for (i = 0; i < ug->u.n; ++i) { // the Segment lines in GFA
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@@ -9424,9 +9439,9 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int print_seq, const char* prefix, FIL
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if(p->m == 0) continue;
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sprintf(name, "%s%.6d%c", prefix, i + 1, "lc"[p->circ]);
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if (print_seq) fprintf(fp, "S\t%s\t%s\tLN:i:%d\trd:i:%u\n", name, p->s? p->s : "*", p->len,
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get_ug_coverage(p, read_g, coverage_cut, sources, ruIndex));
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get_ug_coverage(p, read_g, coverage_cut, sources, ruIndex, primary_flag));
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else fprintf(fp, "S\t%s\t*\tLN:i:%d\trd:i:%u\n", name, p->len,
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get_ug_coverage(p, read_g, coverage_cut, sources, ruIndex));
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get_ug_coverage(p, read_g, coverage_cut, sources, ruIndex, primary_flag));
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// if (print_seq) fprintf(fp, "S\t%s\t%s\tLN:i:%d\n", name, p->s? p->s : "*", p->len);
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// else fprintf(fp, "S\t%s\t*\tLN:i:%d\n", name, p->len);
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@@ -9452,7 +9467,8 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int print_seq, const char* prefix, FIL
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fprintf(fp, "L\t%s%.6d%c\t%c\t%s%.6d%c\t%c\t%dM\tL1:i:%d\n",
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prefix, (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
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prefix, (v>>1)+1, "lc"[ug->u.a[v>>1].circ], "+-"[v&1], ug->g->arc[i].ol, asg_arc_len(ug->g->arc[i]));
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}
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}
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free(primary_flag);
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}
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void ma_ug_print(const ma_ug_t *ug, All_reads *RNF, asg_t* read_g, const ma_sub_t *coverage_cut,
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@@ -11334,6 +11350,45 @@ const char* command)
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}
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uint32_t print_debug_gfa(asg_t *read_g, ma_ug_t *ug, ma_sub_t* coverage_cut, const char* output_file_name,
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ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
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{
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kvec_asg_arc_t_warp new_rtg_edges;
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kv_init(new_rtg_edges.a);
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uint32_t i;
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for (i = 0; i < ug->u.n; ++i)
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{
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ma_utg_t *u = &ug->u.a[i];
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if(u->m == 0 || ug->g->seq[i].c == ALTER_LABLE)
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{
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asg_seq_del(ug->g, i);
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if(ug->u.a[i].m!=0)
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{
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ug->u.a[i].m = ug->u.a[i].n = 0;
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free(ug->u.a[i].a);
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ug->u.a[i].a = NULL;
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}
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}
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}
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ma_ug_seq(ug, read_g, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp);
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fprintf(stderr, "Writing raw unitig GFA to disk... \n");
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char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
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sprintf(gfa_name, "%s.r_utg.noseq.gfa", output_file_name);
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FILE* output_file = fopen(gfa_name, "w");
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ma_ug_print_simple(ug, &R_INF, read_g, coverage_cut, sources, ruIndex, "utg", output_file);
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fclose(output_file);
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free(gfa_name);
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ma_ug_destroy(ug);
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kv_destroy(new_rtg_edges.a);
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exit(0);
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}
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uint32_t print_untig_by_read(ma_ug_t *g, const char* name, uint32_t in, ma_hit_t_alloc* sources,
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ma_hit_t_alloc* reverse_sources, const char* info)
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{
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@@ -11346,6 +11401,7 @@ ma_hit_t_alloc* reverse_sources, const char* info)
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{
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for (i = 0; i < R_INF.total_reads; ++i)
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{
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if(Get_NAME_LENGTH(R_INF, i) != strlen(name)) continue;
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if(memcmp(name, Get_NAME(R_INF, i), Get_NAME_LENGTH(R_INF, i)) == 0)
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{
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fprintf(stderr, "%s: i: %u, >%.*s\n", info, i,
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@@ -11364,7 +11420,7 @@ ma_hit_t_alloc* reverse_sources, const char* info)
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return (uint32_t)-1;
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}
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print_specfic_read_ovlp(rId, sources, reverse_sources, info);
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if(sources && reverse_sources) print_specfic_read_ovlp(rId, sources, reverse_sources, info);
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if(g != NULL)
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{
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@@ -11376,7 +11432,8 @@ ma_hit_t_alloc* reverse_sources, const char* info)
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{
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if(rId == (u->a[k]>>33))
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{
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fprintf(stderr, "%s: %s is the %u-th read at %u-th unitig\n", info, name, k, i);
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fprintf(stderr, "%s: %s is the %u-th read at %u-th unitig (label: %u)\n",
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info, name, k, i, g->g->seq[i].c);
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return i;
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}
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}
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@@ -12165,10 +12222,11 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, uint8_t* r_flag)
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return 0;
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}
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long long R_bases = 0, C_bases = 0, C_bases_primary = 0, C_bases_alter = 0;
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long long total_C_bases = 0, total_C_bases_primary = 0;
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uint32_t available_reads = 0, k, j, rId, tn, is_Unitig;
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ma_hit_t *h;
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if(u->m == 0) return 0;
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available_reads = 0;
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total_C_bases = total_C_bases_primary = available_reads = 0;
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for (k = 0; k < u->n; k++)
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{
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rId = u->a[k]>>33;
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@@ -12202,15 +12260,15 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, uint8_t* r_flag)
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}
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}
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///fprintf(stderr, "C_bases_primary: %lld, C_bases_alter: %lld\n", C_bases_primary, C_bases_alter);
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C_bases = C_bases_primary + C_bases_alter;
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if(C_bases_primary < C_bases * ALTER_COV_THRES) continue;
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total_C_bases += C_bases;
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///if(C_bases_primary < C_bases * ALTER_COV_THRES) continue;
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C_bases = C_bases/R_bases;
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if(C_bases >= asm_opt.recover_atg_cov_min && C_bases <= asm_opt.recover_atg_cov_max)
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{
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available_reads++;
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if(C_bases_primary >= (C_bases_primary + C_bases_alter) * ALTER_COV_THRES) available_reads++;
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total_C_bases_primary += C_bases_primary;
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}
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}
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@@ -12222,13 +12280,14 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, uint8_t* r_flag)
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///fprintf(stderr, "available_reads: %u, u->n: %u\n", available_reads, u->n);
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if(available_reads < (u->n * 0.8) || available_reads == 0)
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//if(available_reads < (u->n * 0.8) || available_reads == 0)
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if(((available_reads < (u->n * 0.8)) && (total_C_bases_primary < (total_C_bases * 0.8)))
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|| available_reads == 0)
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{
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return 0;
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}
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else
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{
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///fprintf(stderr, "*****************\n");
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return 1;
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}
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}
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@@ -12260,12 +12319,39 @@ R_to_U* ruIndex, uint32_t positive_flag, float drop_rate)
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nsu = &(ug->u.a[av[i].v>>1]);
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get_unitig_trio_flag(nsu, flag, &flag_occ, &non_flag_occ, &ambigious);
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///we may need it or not
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if((flag_occ <= ((non_flag_occ+flag_occ)*drop_rate))||
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(flag_occ+non_flag_occ) == 0)
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if((flag_occ <= ((non_flag_occ+flag_occ)*drop_rate))||((flag_occ+non_flag_occ) == 0))
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{
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keep_node++;
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continue;
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}
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}
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if(nsu->n >= 100)
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{
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if(flag_occ < nsu->n*DOUBLE_CHECK_THRES)
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{
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keep_node++;
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continue;
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}
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}
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else if(nsu->n >= 50)
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{
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if(flag_occ < nsu->n*DOUBLE_CHECK_THRES*0.5)
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{
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keep_node++;
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continue;
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}
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}
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else
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{
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if(flag_occ < nsu->n*DOUBLE_CHECK_THRES*0.25)
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{
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keep_node++;
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continue;
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}
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}
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del_node++;
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}
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@@ -12278,12 +12364,33 @@ R_to_U* ruIndex, uint32_t positive_flag, float drop_rate)
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get_unitig_trio_flag(nsu, flag, &flag_occ, &non_flag_occ, &ambigious);
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///we may need it or not
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if((flag_occ <= ((non_flag_occ+flag_occ)*drop_rate))||
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(flag_occ+non_flag_occ) == 0)
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if((flag_occ <= ((non_flag_occ+flag_occ)*drop_rate))||((flag_occ+non_flag_occ) == 0))
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{
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continue;
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}
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if(nsu->n >= 100)
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{
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if(flag_occ < nsu->n*DOUBLE_CHECK_THRES)
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{
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continue;
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}
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}
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else if(nsu->n >= 50)
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{
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if(flag_occ < nsu->n*DOUBLE_CHECK_THRES*0.5)
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{
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continue;
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}
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}
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else
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{
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if(flag_occ < nsu->n*DOUBLE_CHECK_THRES*0.25)
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{
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continue;
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}
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}
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if(if_primary_unitig(nsu, read_sg, coverage_cut, sources, ruIndex, primary_flag))
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{
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continue;
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@@ -12435,7 +12542,7 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen, uint32_t stops_threshold
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R_to_U* ruIndex)
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{
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double startTime = Get_T();
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uint32_t i, k, v_i, v_beg, v_end, selfLen, w1, w2, wv, nw, n_vtx = g->n_seq * 2, n_reduced = 0, convex, convex_T;
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uint32_t i, k, v_i, v_beg, v_end, selfLen, w1, w2, wv, nw, n_vtx = g->n_seq * 2, n_reduced = 0, convex, convex_T, read_num;
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asg_arc_t *aw;
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long long ll, tmp, max_stop_nodeLen, max_stop_baseLen;
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@@ -12508,7 +12615,7 @@ R_to_U* ruIndex)
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///if(convex == convex_T) break;
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for (k = 0; k < b_0.b.n; k++)
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{
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if(b_0.b.a[k] == (convex_T>>1)) break;
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if((b_0.b.a[k]>>1) == (convex_T>>1)) break;
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}
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if(k != b_0.b.n) break;
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@@ -12554,7 +12661,7 @@ R_to_U* ruIndex)
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///if(convex == convex_T) break;
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for (k = 0; k < b_0.b.n; k++)
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{
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if(b_0.b.a[k] == (convex_T>>1)) break;
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if((b_0.b.a[k]>>1) == (convex_T>>1)) break;
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}
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if(k != b_0.b.n) break;
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@@ -12566,17 +12673,15 @@ R_to_U* ruIndex)
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}
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if(i!=nw) continue;
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n_reduced++;
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b_0.b.n = 0;
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read_num = 0;
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///get_long_tip_length(g, &(ug->u), v_beg^1, &v_end, &b_0);
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get_unitig(g, ug, v_beg^1, &v_end, &ll, &tmp, &max_stop_nodeLen, &max_stop_baseLen, 1, &b_0);
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for (k = 0; k < b_0.b.n; k++)
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{
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g->seq[b_0.b.a[k]>>1].c = ALTER_LABLE;
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read_num += ug->u.a[b_0.b.a[k]>>1].n;
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}
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for (k = 0; k < b_0.b.n; k++)
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@@ -12584,6 +12689,14 @@ R_to_U* ruIndex)
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asg_seq_drop(g, b_0.b.a[k]>>1);
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}
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if(read_num <= CHIMERIC_TRIM_THRES)
|
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{
|
||||
for (k = 0; k < b_0.b.n; k++)
|
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{
|
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g->seq[b_0.b.a[k]>>1].c = CUT;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
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asg_cleanup(g);
|
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@@ -12756,12 +12869,29 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
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uint32_t is_first = 1;
|
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|
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redo:
|
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///if(trio_flag == MOTHER) fprintf(stderr, "(0) c: %u, del: %u, n: %u\n", ug->g->seq[28141].c, ug->g->seq[28141].del, ug->u.a[28141].n);
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|
||||
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print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "beg");
|
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print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "beg");
|
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|
||||
|
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asg_pop_bubble_primary_trio(ug, bubble_dist, trio_flag, DROP);
|
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|
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print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "beg-1");
|
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print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "beg-1");
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untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, trio_flag, DROP);
|
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|
||||
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "beg-2");
|
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print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "beg-2");
|
||||
|
||||
magic_trio_phasing(g, ug, read_g, coverage_cut, sources, reverse_sources, 2, ruIndex, trio_flag, trio_drop_rate);
|
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///drop_semi_circle(ug, g, read_g, reverse_sources, ruIndex);
|
||||
|
||||
|
||||
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "111");
|
||||
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "111");
|
||||
|
||||
|
||||
/**********debug**********/
|
||||
if(just_bubble_pop == 0)
|
||||
{
|
||||
@@ -12779,6 +12909,9 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
|
||||
long long cur_cons = 0;
|
||||
while(pre_cons != cur_cons)
|
||||
{
|
||||
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "222");
|
||||
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "222");
|
||||
|
||||
pre_cons = get_graph_statistic(g);
|
||||
///need consider tangles
|
||||
///asg_pop_bubble_primary(g, bubble_dist);
|
||||
@@ -12790,16 +12923,38 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
|
||||
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex,
|
||||
2, tip_drop_ratio);
|
||||
|
||||
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "333");
|
||||
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "333");
|
||||
|
||||
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, trio_flag);
|
||||
|
||||
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "444");
|
||||
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "444");
|
||||
|
||||
|
||||
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex,
|
||||
2, tip_drop_ratio, stops_threshold);
|
||||
|
||||
|
||||
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "555");
|
||||
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "555");
|
||||
|
||||
|
||||
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources,
|
||||
2, ruIndex, stops_threshold);
|
||||
|
||||
|
||||
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "666");
|
||||
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "666");
|
||||
|
||||
///print_debug_gfa(read_g, ug, coverage_cut, "debug_chimeric", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
|
||||
|
||||
|
||||
detect_chimeric_by_topo(g, ug, read_g, reverse_sources, 2, stops_threshold, chimeric_rate,
|
||||
ruIndex);
|
||||
|
||||
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "666-2");
|
||||
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "666-2");
|
||||
///need consider tangles
|
||||
///note we need both the read graph and the untig graph
|
||||
}
|
||||
@@ -12808,6 +12963,9 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
|
||||
}
|
||||
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, trio_flag, DROP);
|
||||
|
||||
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "777");
|
||||
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "777");
|
||||
|
||||
if(just_bubble_pop == 0)
|
||||
{
|
||||
///asg_cut_tip_primary(g, ug, tipsLen);
|
||||
@@ -12815,9 +12973,25 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
|
||||
2);
|
||||
}
|
||||
|
||||
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "888");
|
||||
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "888");
|
||||
|
||||
resolve_tangles(ug, read_g, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, trio_flag, drop_ratio);
|
||||
|
||||
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "999");
|
||||
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "999");
|
||||
|
||||
drop_semi_circle(ug, g, read_g, reverse_sources, ruIndex);
|
||||
all_to_all_deduplicate(ug, read_g, coverage_cut, sources, trio_flag, trio_drop_rate, reverse_sources, ruIndex);
|
||||
|
||||
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "101010");
|
||||
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "101010");
|
||||
|
||||
|
||||
all_to_all_deduplicate(ug, read_g, coverage_cut, sources, trio_flag, trio_drop_rate, reverse_sources, ruIndex, DOUBLE_CHECK_THRES);
|
||||
|
||||
print_untig_by_read(ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "111111");
|
||||
print_untig_by_read(ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "111111");
|
||||
|
||||
|
||||
if(is_first)
|
||||
{
|
||||
@@ -12928,7 +13102,7 @@ void set_drop_trio_flag(ma_ug_t *ug)
|
||||
|
||||
void update_unitig_graph(ma_ug_t* ug, asg_t* read_g, ma_sub_t* coverage_cut,
|
||||
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex,
|
||||
uint8_t is_double_check, uint8_t flag, float drop_rate)
|
||||
uint8_t is_final_check, float double_check_rate, uint8_t flag, float drop_rate)
|
||||
{
|
||||
asg_t* nsg = ug->g;
|
||||
uint32_t v, n_vtx = nsg->n_seq, k, rId, flag_occ, non_flag_occ, hap_label_occ, n_reduce = 1;
|
||||
@@ -12961,14 +13135,44 @@ uint8_t is_double_check, uint8_t flag, float drop_rate)
|
||||
}
|
||||
|
||||
if(hap_label_occ == u->n) continue;
|
||||
if(is_double_check && non_flag_occ < u->n*DOUBLE_CHECK_THRES) continue;
|
||||
///if(is_double_check && non_flag_occ < u->n*DOUBLE_CHECK_THRES) continue;
|
||||
///if(is_double_check && non_flag_occ < u->n*double_check_rate) continue;
|
||||
if(is_final_check)
|
||||
{
|
||||
if(non_flag_occ < u->n*double_check_rate) continue;
|
||||
}
|
||||
else
|
||||
{
|
||||
if(u->n >= 100)
|
||||
{
|
||||
if(non_flag_occ < u->n*double_check_rate)
|
||||
{
|
||||
continue;
|
||||
}
|
||||
}
|
||||
else if(u->n >= 50)
|
||||
{
|
||||
if(non_flag_occ < u->n*double_check_rate*0.5)
|
||||
{
|
||||
continue;
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
if(non_flag_occ < u->n*double_check_rate*0.25)
|
||||
{
|
||||
continue;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
if(non_flag_occ > ((non_flag_occ+flag_occ)*drop_rate))
|
||||
{
|
||||
if(if_primary_unitig(u, read_g, coverage_cut, sources, ruIndex, primary_flag))
|
||||
{
|
||||
continue;
|
||||
}
|
||||
}
|
||||
if(u->m != 0)
|
||||
{
|
||||
u->circ = u->end = u->len = u->m = u->n = u->start = 0;
|
||||
@@ -13109,7 +13313,7 @@ uint32_t* non_require, uint32_t* ambigious)
|
||||
///note: to use this function, don't renew unitig graph!!!!!!!!!
|
||||
void all_to_all_deduplicate(ma_ug_t* ug, asg_t* read_g, ma_sub_t* coverage_cut,
|
||||
ma_hit_t_alloc* sources, uint8_t postive_flag, float drop_rate,
|
||||
ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex)
|
||||
ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, float double_check_rate)
|
||||
{
|
||||
|
||||
|
||||
@@ -13170,6 +13374,27 @@ ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex)
|
||||
///we may need it or not
|
||||
if(flag_occ <= ((non_flag_occ+flag_occ)*drop_rate)) continue;
|
||||
if((flag_occ+non_flag_occ) == 0) continue;
|
||||
if(nsu->n >= 100)
|
||||
{
|
||||
if(flag_occ < nsu->n*double_check_rate)
|
||||
{
|
||||
continue;
|
||||
}
|
||||
}
|
||||
else if(nsu->n >= 50)
|
||||
{
|
||||
if(flag_occ < nsu->n*double_check_rate*0.5)
|
||||
{
|
||||
continue;
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
if(flag_occ < nsu->n*double_check_rate*0.25)
|
||||
{
|
||||
continue;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@@ -13491,6 +13716,14 @@ long long bubble_dist, long long tipsLen, float tip_drop_ratio, long long stops_
|
||||
R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp,
|
||||
kvec_asg_arc_t_warp* new_rtg_edges)
|
||||
{
|
||||
// if(flag == MOTHER)
|
||||
// {
|
||||
// print_debug_gfa(read_g, *ug, coverage_cut, "debug_hap2", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
|
||||
// }
|
||||
|
||||
print_untig_by_read(*ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "0-beg");
|
||||
print_untig_by_read(*ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "0-beg");
|
||||
|
||||
asg_t* nsg = (*ug)->g;
|
||||
uint32_t v, n_vtx = nsg->n_seq;
|
||||
//if(flag == MOTHER) print_untig_by_read(*ug, "m54329U_190617_231905/65340614/ccs", (uint32_t)-1, sources, reverse_sources, "beg1");
|
||||
@@ -13526,7 +13759,12 @@ kvec_asg_arc_t_warp* new_rtg_edges)
|
||||
///primary_flag = get_utg_attributes(*ug, read_g, coverage_cut, sources, ruIndex);
|
||||
|
||||
|
||||
update_unitig_graph((*ug), read_g, coverage_cut, sources, reverse_sources, ruIndex, 0, flag, drop_rate);
|
||||
update_unitig_graph((*ug), read_g, coverage_cut, sources, reverse_sources, ruIndex, 0,
|
||||
DOUBLE_CHECK_THRES, flag, drop_rate);
|
||||
|
||||
print_untig_by_read(*ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "1-beg");
|
||||
print_untig_by_read(*ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "1-beg");
|
||||
|
||||
adjust_utg_advance(read_g, (*ug), reverse_sources, ruIndex);
|
||||
nsg = (*ug)->g;
|
||||
n_vtx = nsg->n_seq;
|
||||
@@ -13537,6 +13775,9 @@ kvec_asg_arc_t_warp* new_rtg_edges)
|
||||
EvaluateLen((*ug)->u, v) = (*ug)->u.a[v].n;
|
||||
}
|
||||
|
||||
print_untig_by_read(*ug, "m54329U_190619_052546/130155526/ccs", 3323601, NULL, NULL, "2-beg");
|
||||
print_untig_by_read(*ug, "m54329U_190827_173812/131008083/ccs", 7014763, NULL, NULL, "2-beg");
|
||||
|
||||
clean_trio_untig_graph(*ug, read_g, coverage_cut, sources, reverse_sources, bubble_dist,
|
||||
tipsLen, tip_drop_ratio, stops_threshold, ruIndex, NULL, NULL, 0, 0, 0,
|
||||
chimeric_rate, 0, 0, drop_ratio, flag, drop_rate);
|
||||
@@ -13548,7 +13789,8 @@ kvec_asg_arc_t_warp* new_rtg_edges)
|
||||
|
||||
update_hap_label(*ug, read_g);
|
||||
|
||||
update_unitig_graph((*ug), read_g, coverage_cut, sources, reverse_sources, ruIndex, 0, flag, drop_rate);
|
||||
update_unitig_graph((*ug), read_g, coverage_cut, sources, reverse_sources, ruIndex, 0,
|
||||
DOUBLE_CHECK_THRES, flag, drop_rate);
|
||||
|
||||
renew_utg(ug, read_g, new_rtg_edges);
|
||||
|
||||
@@ -13565,7 +13807,8 @@ kvec_asg_arc_t_warp* new_rtg_edges)
|
||||
renew_utg(ug, read_g, new_rtg_edges);
|
||||
}
|
||||
|
||||
update_unitig_graph((*ug), read_g, coverage_cut, sources, reverse_sources, ruIndex, 1, flag, drop_rate);
|
||||
update_unitig_graph((*ug), read_g, coverage_cut, sources, reverse_sources, ruIndex, 1,
|
||||
FINAL_DOUBLE_CHECK_THRES, flag, drop_rate);
|
||||
|
||||
update_hap_label(NULL, read_g);
|
||||
|
||||
@@ -22432,14 +22675,18 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex)
|
||||
uint32_t v, n_vtx = nsg->n_seq, k, j, rId, available_reads = 0, keep_atg = 0, tn, is_Unitig;
|
||||
ma_utg_t* u = NULL;
|
||||
ma_hit_t *h;
|
||||
|
||||
|
||||
///print_untig_by_read(atg, "SRR11606870.634978", -1, NULL, NULL, "debug");
|
||||
long long R_bases = 0, C_bases = 0, C_bases_primary = 0, C_bases_alter = 0;
|
||||
long long total_C_bases = 0, total_C_bases_alter = 0;
|
||||
for (v = 0; v < n_vtx; ++v)
|
||||
{
|
||||
if(nsg->seq[v].del) continue;
|
||||
u = &(atg->u.a[v]);
|
||||
if(u->m == 0) continue;
|
||||
available_reads = 0;
|
||||
|
||||
total_C_bases = total_C_bases_alter = available_reads = 0;
|
||||
|
||||
for (k = 0; k < u->n; k++)
|
||||
{
|
||||
rId = u->a[k]>>33;
|
||||
@@ -22468,16 +22715,19 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex)
|
||||
}
|
||||
|
||||
C_bases = C_bases_primary + C_bases_alter;
|
||||
if(C_bases_alter < C_bases * ALTER_COV_THRES) continue;
|
||||
total_C_bases += C_bases;
|
||||
|
||||
C_bases = C_bases/R_bases;
|
||||
if(C_bases >= asm_opt.recover_atg_cov_min && C_bases <= asm_opt.recover_atg_cov_max)
|
||||
{
|
||||
available_reads++;
|
||||
if(C_bases_alter >= (C_bases_primary + C_bases_alter) * ALTER_COV_THRES) available_reads++;
|
||||
total_C_bases_alter += C_bases_alter;
|
||||
}
|
||||
}
|
||||
|
||||
if(available_reads < (u->n * 0.8) || available_reads == 0)
|
||||
|
||||
if(((available_reads < (u->n * 0.8)) && (total_C_bases_alter < (total_C_bases * 0.8)))
|
||||
|| available_reads == 0)
|
||||
{
|
||||
asg_seq_del(nsg, v);
|
||||
|
||||
|
||||
Reference in New Issue
Block a user