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508 —> futhur graph cleaning

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chhylp123
2023-02-12 22:49:12 -05:00
parent 1166b92eb4
commit f2da12a2ad
13 changed files with 4422 additions and 110 deletions
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Overlaps.cpp
+128 -43
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@@ -64,6 +64,7 @@ KSORT_INIT_GENERIC(uint32_t)
void reduce_hamming_error_adv(ma_ug_t *iug, asg_t *sg, ma_hit_t_alloc* sources, ma_sub_t *coverage_cut,
int max_hang, int min_ovlp, long long gap_fuzz, R_to_U *ru, bubble_type* bub);
void print_vw_edge(asg_t *sg, uint32_t vid, uint32_t wid, const char *cmd);
typedef struct {
uint32_t d, tot, ma, p;
@@ -10101,13 +10102,29 @@ uint64_t *n_utg)
return C_bases/R_bases;
}
uint32_t cal_circle_ov(const ma_ug_t *ug, uint32_t uid, uint32_t rev, asg_t *sg)
{
uint32_t v, w, vx, wx, k;
v = w = (uid<<1)+(!!rev);
vx = (v&1?((ug->u.a[v>>1].a[0]>>32)^1):(ug->u.a[v>>1].a[ug->u.a[v>>1].n-1]>>32));
wx = (w&1?((ug->u.a[w>>1].a[ug->u.a[w>>1].n-1]>>32)^1):(ug->u.a[w>>1].a[0]>>32));
v = vx; w = wx;
if(sg) {
asg_arc_t *av; uint32_t nv;
av = asg_arc_a(sg, vx); nv = asg_arc_n(sg, vx);
for (k = 0; k < nv; k++) {
if(av[k].v == wx) return av[k].ol;
}
}
return 0;
}
void ma_ug_print2(const ma_ug_t *ug, All_reads *RNF, asg_t* read_g, const ma_sub_t *coverage_cut,
ma_hit_t_alloc* sources, R_to_U* ruIndex, int print_seq, const char* prefix, FILE *fp)
{
uint8_t* primary_flag = read_g?(uint8_t*)calloc(read_g->n_seq, sizeof(uint8_t)):NULL;
uint32_t i, j, l, pc = read_g && coverage_cut && sources && ruIndex?1:0;
uint32_t i, j, l, pc = read_g && coverage_cut && sources && ruIndex?1:0, co;
char name[32];
for (i = 0; i < ug->u.n; ++i) { // the Segment lines in GFA
ma_utg_t *p = &ug->u.a[i];
@@ -10154,37 +10171,39 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int print_seq, const char* prefix, FIL
uint32_t nu, u, v;
for (i = 0; i < ug->u.n; ++i) {
if(ug->u.a[i].m == 0) continue;
if(ug->u.a[i].circ)
{
fprintf(fp, "L\t%s%.6dc\t+\t%s%.6dc\t+\t%dM\tL1:i:%d\n",
prefix, i+1, prefix, i+1, 0, ug->u.a[i].len);
fprintf(fp, "L\t%s%.6dc\t-\t%s%.6dc\t-\t%dM\tL1:i:%d\n",
prefix, i+1, prefix, i+1, 0, ug->u.a[i].len);
if(ug->u.a[i].circ) {
co = cal_circle_ov(ug, i, 0, read_g);
fprintf(fp, "L\t%s%.6dc\t+\t%s%.6dc\t+\t%dM\tL1:i:%d\tL2:i:%u\n",
prefix, i+1, prefix, i+1, co, ((ug->u.a[i].len>=co)?(ug->u.a[i].len-co):0), 0);
co = cal_circle_ov(ug, i, 1, read_g);
fprintf(fp, "L\t%s%.6dc\t-\t%s%.6dc\t-\t%dM\tL1:i:%d\tL2:i:%u\n",
prefix, i+1, prefix, i+1, co, ((ug->u.a[i].len>=co)?(ug->u.a[i].len-co):0), 0);
} else {
u = i<<1;
au = asg_arc_a(ug->g, u);
nu = asg_arc_n(ug->g, u);
for (j = 0; j < nu; j++)
{
if(au[j].del) continue;
v = au[j].v;
fprintf(fp, "L\t%s%.6d%c\t%c\t%s%.6d%c\t%c\t%dM\tL1:i:%d\tL2:i:%u\n",
prefix, (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
prefix, (v>>1)+1, "lc"[ug->u.a[v>>1].circ], "+-"[v&1], au[j].ol, asg_arc_len(au[j]), 0/**au[j].ou**/);
}
u = (i<<1) + 1;
au = asg_arc_a(ug->g, u);
nu = asg_arc_n(ug->g, u);
for (j = 0; j < nu; j++)
{
if(au[j].del) continue;
v = au[j].v;
fprintf(fp, "L\t%s%.6d%c\t%c\t%s%.6d%c\t%c\t%dM\tL1:i:%d\tL2:i:%u\n",
prefix, (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
prefix, (v>>1)+1, "lc"[ug->u.a[v>>1].circ], "+-"[v&1], au[j].ol, asg_arc_len(au[j]), 0/**au[j].ou**/);
}
}
u = i<<1;
au = asg_arc_a(ug->g, u);
nu = asg_arc_n(ug->g, u);
for (j = 0; j < nu; j++)
{
if(au[j].del) continue;
v = au[j].v;
fprintf(fp, "L\t%s%.6d%c\t%c\t%s%.6d%c\t%c\t%dM\tL1:i:%d\tL2:i:%u\n",
prefix, (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
prefix, (v>>1)+1, "lc"[ug->u.a[v>>1].circ], "+-"[v&1], au[j].ol, asg_arc_len(au[j]), 0/**au[j].ou**/);
}
u = (i<<1) + 1;
au = asg_arc_a(ug->g, u);
nu = asg_arc_n(ug->g, u);
for (j = 0; j < nu; j++)
{
if(au[j].del) continue;
v = au[j].v;
fprintf(fp, "L\t%s%.6d%c\t%c\t%s%.6d%c\t%c\t%dM\tL1:i:%d\tL2:i:%u\n",
prefix, (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
prefix, (v>>1)+1, "lc"[ug->u.a[v>>1].circ], "+-"[v&1], au[j].ol, asg_arc_len(au[j]), 0/**au[j].ou**/);
}
}
}
free(primary_flag);
@@ -13494,12 +13513,16 @@ void hic_clean(asg_t* read_g)
void hic_clean_adv(asg_t *sg, ug_opt_t *uopt)
{
uint32_t i, k, m, z, v, w; ma_utg_t *u = NULL; uint32_t *ba, bn, n_vtx, beg, end, n0, n1;
uint32_t i, k, m, z, v, w, mk; ma_utg_t *u = NULL; uint32_t *ba, bn, n_vtx, beg, end, n0, n1; ma_utg_t *mz = NULL;
ma_ug_t *ug = ma_ug_gen_primary(sg, PRIMARY_LABLE); n_vtx = ug->g->n_seq<<1; double bub_rate = 0.1;
uint8_t *bf = NULL; bubble_type *bub = gen_bubble_chain(sg, ug, uopt, &bf);
uint64_t tLen, vocc, socc, pocc; buf_t b; memset(&b, 0, sizeof(buf_t)); CALLOC(b.a, n_vtx);
REALLOC(bf, n_vtx); memset(bf, 0, sizeof((*bf))*n_vtx);
kvec_t(uint64_t) buf; kv_init(buf); n0 = n1 = 0;
for (i = 0; i < ug->g->n_seq; ++i) {
if(ug->g->seq[i].del) continue;
ug->g->seq[i].c = PRIMARY_LABLE;
}
for (i = 0; i < bub->b_ug->u.n; i++) {
u = &(bub->b_ug->u.a[i]);
@@ -13568,6 +13591,20 @@ void hic_clean_adv(asg_t *sg, ug_opt_t *uopt)
if((pocc+socc) >= (vocc*bub_rate)) continue;
pocc += socc;
asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 1, NULL, NULL, NULL, 0, 0, NULL);
for (z = 0; z < b.b.n; z++) {
if(b.b.a[z]==v || b.b.a[z]==b.S.a[0]) continue;
// socc += ug->u.a[b.b.a[i]>>1].n;
if(ug->g->seq[b.b.a[z]>>1].del) continue;
if(ug->g->seq[b.b.a[z]>>1].c != ALTER_LABLE) continue;
mz = &(ug->u.a[b.b.a[z]>>1]);
if(mz->m == 0) continue;
for (mk = 0; mk < mz->n; mk++) asg_seq_del(sg, mz->a[mk]>>33);
asg_seq_del(ug->g, b.b.a[z]>>1);
if(ug->u.a[b.b.a[z]>>1].m) {
ug->u.a[b.b.a[z]>>1].m = ug->u.a[b.b.a[z]>>1].n = 0;
free(ug->u.a[b.b.a[z]>>1].a); ug->u.a[b.b.a[z]>>1].a = NULL;
}
}
// fprintf(stderr, "+utg%.6dl\tutg%.6dl\n", (int32_t)(v>>1)+1, (int32_t)(b.S.a[0]>>1)+1);
n0++;
}
@@ -13579,6 +13616,22 @@ void hic_clean_adv(asg_t *sg, ug_opt_t *uopt)
}
}
for (v = 0; v < ug->g->n_seq; ++v) {
if(ug->g->seq[v].del) continue;
if(ug->g->seq[v].c != ALTER_LABLE) continue;
mz = &(ug->u.a[v]);
if(mz->m == 0) continue;
for (k = 0; k < mz->n; k++) asg_seq_del(sg, mz->a[k]>>33);
asg_seq_del(ug->g, v);
if(ug->u.a[v].m) {
ug->u.a[v].m = ug->u.a[v].n = 0;
free(ug->u.a[v].a); ug->u.a[v].a = NULL;
}
}
asg_cleanup(ug->g);
tLen = get_bub_pop_max_dist_advance(ug->g, &b);
for (v = buf.n = 0; v < n_vtx; ++v) {
if(ug->g->seq[v>>1].del) continue;
@@ -13624,14 +13677,43 @@ void hic_clean_adv(asg_t *sg, ug_opt_t *uopt)
vocc += ug->u.a[b.b.a[k]>>1].n;
}
if((socc) >= (vocc*bub_rate)) continue;
asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 1, NULL, NULL, NULL, 0, 0, NULL);
for (i = 0; i < b.b.n; i++) {
if(b.b.a[i]==v || b.b.a[i]==b.S.a[0]) continue;
// socc += ug->u.a[b.b.a[i]>>1].n;
if(ug->g->seq[b.b.a[i]>>1].del) continue;
if(ug->g->seq[b.b.a[i]>>1].c != ALTER_LABLE) continue;
mz = &(ug->u.a[b.b.a[i]>>1]);
if(mz->m == 0) continue;
for (mk = 0; mk < mz->n; mk++) asg_seq_del(sg, mz->a[mk]>>33);
asg_seq_del(ug->g, b.b.a[i]>>1);
if(ug->u.a[b.b.a[i]>>1].m) {
ug->u.a[b.b.a[i]>>1].m = ug->u.a[b.b.a[i]>>1].n = 0;
free(ug->u.a[b.b.a[i]>>1].a); ug->u.a[b.b.a[i]>>1].a = NULL;
}
}
// fprintf(stderr, "-utg%.6dl\tutg%.6dl\n", (int32_t)(v>>1)+1, (int32_t)(b.S.a[0]>>1)+1);
n1++;
}
}
}
filter_sg_by_ug(sg, ug, uopt);
// filter_sg_by_ug(sg, ug, uopt);
for (v = 0; v < ug->g->n_seq; ++v) {
if(ug->g->seq[v].del) continue;
if(ug->g->seq[v].c != ALTER_LABLE) continue;
mz = &(ug->u.a[v]);
if(mz->m == 0) continue;
for (k = 0; k < mz->n; k++) asg_seq_del(sg, mz->a[k]>>33);
asg_seq_del(ug->g, v);
if(ug->u.a[v].m) {
ug->u.a[v].m = ug->u.a[v].n = 0;
free(ug->u.a[v].a); ug->u.a[v].a = NULL;
}
}
asg_cleanup(ug->g);
asg_cleanup(sg);
free(b.a); free(b.S.a); free(b.T.a); free(b.b.a); free(b.e.a);
ma_ug_destroy(ug); free(bf); kv_destroy(buf);
destory_bubbles(bub); free(bub);
@@ -15627,7 +15709,6 @@ bub_label_t* b_mask_t)
ma_ug_t *ug = NULL;
ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
hap_cov_t *cov = NULL;
asg_t *copy_sg = copy_read_graph(sg);
ma_ug_t *copy_ug = copy_untig_graph(ug);
@@ -27603,7 +27684,7 @@ R_to_U* ruIndex, int max_hang, int min_ovlp, kvec_asg_arc_t_warp* new_rtg_edges,
void output_contig_graph_primary_pre(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, uint64_t bubble_dist, long long tipsLen,
R_to_U* ruIndex, int max_hang, int min_ovlp)
R_to_U* ruIndex, int max_hang, int min_ovlp, const ug_opt_t *uopt)
{
kvec_asg_arc_t_warp new_rtg_edges;
kv_init(new_rtg_edges.a);
@@ -27656,6 +27737,10 @@ R_to_U* ruIndex, int max_hang, int min_ovlp)
fclose(output_file);
}
///for debug
// graph_ovlp_binning(ug, sg, uopt);
// gen_hpc_re_t(ug);
free(gfa_name);
ma_ug_destroy(ug);
kv_destroy(new_rtg_edges.a);
@@ -33584,10 +33669,10 @@ ma_hit_t_alloc* src, uint64_t* readLen, R_to_U* ruIndex, bub_label_t *b_mask_t,
}
void renew_g(ma_hit_t_alloc **sources, ma_hit_t_alloc **reverse_sources, long long *n_read,
uint64_t **readLen, ma_sub_t **coverage_cut, R_to_U *ruIndex, asg_t **sg,
int64_t mini_overlap_length, int64_t max_hang_length,
ug_opt_t *uopt, int64_t clean_round, double min_ovlp_drop_ratio, double max_ovlp_drop_ratio,
int64_t max_tip, bub_label_t *b_mask_t, uint32_t is_trio, char *o_file, const char *bin_file, uint64_t free_uld)
uint64_t **readLen, ma_sub_t **coverage_cut, R_to_U *ruIndex, asg_t **sg, int64_t mini_overlap_length,
int64_t max_hang_length, ug_opt_t *uopt, int64_t clean_round, double min_ovlp_drop_ratio,
double max_ovlp_drop_ratio, int64_t max_tip, bub_label_t *b_mask_t, uint32_t is_trio,
char *o_file, const char *bin_file, uint64_t free_uld, uint64_t is_bridg, uint64_t deep_clean)
{
ul_renew_t nopt; memset(&nopt, 0, sizeof(nopt));
nopt.src = sources; nopt.r_src = reverse_sources; nopt.ruIndex = ruIndex;
@@ -33595,7 +33680,7 @@ int64_t max_tip, bub_label_t *b_mask_t, uint32_t is_trio, char *o_file, const ch
nopt.cov = coverage_cut; nopt.b_mask_t = b_mask_t;
nopt.max_hang = max_hang_length; nopt.mini_ovlp = mini_overlap_length;
ul_realignment_gfa(uopt, *sg, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
asm_opt.max_short_tip, asm_opt.max_short_ul_tip, b_mask_t, ha_opt_triobin(&asm_opt), o_file, &nopt, bin_file, free_uld);
asm_opt.max_short_tip, asm_opt.max_short_ul_tip, b_mask_t, ha_opt_triobin(&asm_opt), o_file, &nopt, bin_file, free_uld, is_bridg, deep_clean);
// ma_ug_t *iug = ul_realignment_gfa(uopt, *sg, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
// asm_opt.max_short_tip, b_mask_t, ha_opt_triobin(&asm_opt), o_file);
// asg_t *ng = gen_ng(iug, *sg, uopt, coverage_cut, ruIndex, 256);
@@ -33618,7 +33703,7 @@ bub_label_t *b_mask_t, uint32_t is_trio, int32_t ul_aln_round, char *o_file, con
int32_t k, strl = strlen(bin_file)+1, kt, cl, sl; char *id = NULL;
renew_g(src, rev_src, n_read, readLen, cov, ruIndex, sg, mini_overlap_length, max_hang_length,
uopt, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio, asm_opt.max_short_tip, b_mask_t,
is_trio, o_file, bin_file, (ul_aln_round<=1)?1:0);
is_trio, o_file, bin_file, (ul_aln_round<=1)?1:0, 1, 1);
gen_ug_opt_t(uopt, *src, *rev_src, max_hang_length, mini_overlap_length, gap_fuzz, min_dp, *readLen,
*cov, ruIndex, (asm_opt.max_short_tip*2), 0.15, 3, 0.05, 0.9, b_mask_t);
ug_ext_gfa(uopt, *sg, ug_ext_len);
@@ -33634,7 +33719,7 @@ bub_label_t *b_mask_t, uint32_t is_trio, int32_t ul_aln_round, char *o_file, con
sprintf(id, "%s%d", bin_file, k);
renew_g(src, rev_src, n_read, readLen, cov, ruIndex, sg, mini_overlap_length, max_hang_length,
uopt, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio, asm_opt.max_short_tip, b_mask_t,
is_trio, o_file, id, ((k+1)==ul_aln_round)?1:0);
is_trio, o_file, id, ((k+1)==ul_aln_round)?1:0, 0, 0);
gen_ug_opt_t(uopt, *src, *rev_src, max_hang_length, mini_overlap_length, gap_fuzz, min_dp, *readLen,
*cov, ruIndex, (asm_opt.max_short_tip*2), 0.15, 3, 0.05, 0.9, b_mask_t);
ug_ext_gfa(uopt, *sg, ug_ext_len);
@@ -33902,7 +33987,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
**/
output_contig_graph_primary_pre(sg, coverage_cut, o_file, sources, reverse_sources,
asm_opt.small_pop_bubble_size, asm_opt.max_short_tip, ruIndex, max_hang_length, mini_overlap_length);
asm_opt.small_pop_bubble_size, asm_opt.max_short_tip, ruIndex, max_hang_length, mini_overlap_length, &uopt);
/**
if (asm_opt.flag & HA_F_VERBOSE_GFA)
{