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resolve centromere

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chhylp123
2021-05-06 07:59:51 -04:00
parent 24e5453781
commit 9ea4f6917f
5 changed files with 163 additions and 67 deletions
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Overlaps.cpp
+27 -33
View File
@@ -8994,8 +8994,8 @@ UC_Read* r_read, UC_Read* q_read, int max_hang, int min_ovlp, kvec_asg_arc_t_war
// generate unitig sequences // generate unitig sequences
int ma_ug_seq(ma_ug_t *g, asg_t *read_g, All_reads *RNF, ma_sub_t *coverage_cut, int ma_ug_seq(ma_ug_t *g, asg_t *read_g, ma_sub_t *coverage_cut, ma_hit_t_alloc* sources,
ma_hit_t_alloc* sources, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp, kvec_asg_arc_t_warp *E) kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp, kvec_asg_arc_t_warp *E, uint32_t is_polish)
{ {
UC_Read g_read; UC_Read g_read;
init_UC_Read(&g_read); init_UC_Read(&g_read);
@@ -9013,8 +9013,12 @@ ma_hit_t_alloc* sources, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp,
for (i = 0; i < g->u.n; ++i) { for (i = 0; i < g->u.n; ++i) {
ma_utg_t *u = &g->u.a[i]; ma_utg_t *u = &g->u.a[i];
if(u->m == 0) continue; if(u->m == 0) continue;
polish_unitig(u, read_g, sources, coverage_cut, edge, max_hang, min_ovlp, E); if(is_polish)
polish_unitig_advance(u, read_g, RNF, sources, coverage_cut, edge, &g_read, &tmp, max_hang, min_ovlp, E); {
polish_unitig(u, read_g, sources, coverage_cut, edge, max_hang, min_ovlp, E);
polish_unitig_advance(u, read_g, &R_INF, sources, coverage_cut, edge, &g_read, &tmp, max_hang, min_ovlp, E);
}
g->g->seq[i].len = u->len; g->g->seq[i].len = u->len;
uint32_t l = 0; uint32_t l = 0;
@@ -9031,12 +9035,12 @@ ma_hit_t_alloc* sources, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp,
if(eLen == 0) continue; if(eLen == 0) continue;
if(rId < read_g->r_seq) if(rId < read_g->r_seq)
{ {
recover_UC_Read(&g_read, RNF, rId); recover_UC_Read(&g_read, &R_INF, rId);
} }
else else
{ {
recover_fake_read(&g_read, &tmp, &(read_g->F_seq[rId-read_g->r_seq]), recover_fake_read(&g_read, &tmp, &(read_g->F_seq[rId-read_g->r_seq]),
RNF, coverage_cut); &R_INF, coverage_cut);
} }
readS = g_read.seq + coverage_cut[rId].s; readS = g_read.seq + coverage_cut[rId].s;
@@ -12153,7 +12157,7 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
ma_ug_t *ug = NULL; ma_ug_t *ug = NULL;
ug = ma_ug_gen(sg); ug = ma_ug_gen(sg);
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0); ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
fprintf(stderr, "Writing raw unitig GFA to disk... \n"); fprintf(stderr, "Writing raw unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+25); char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
@@ -12493,7 +12497,7 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp, kvec_asg_a
NULL, &asm_opt.b_high_cov, asm_opt.m_rate); NULL, &asm_opt.b_high_cov, asm_opt.m_rate);
} }
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, new_rtg_edges, max_hang, min_ovlp, 0); ma_ug_seq(ug, sg, coverage_cut, sources, new_rtg_edges, max_hang, min_ovlp, 0, 1);
char* gfa_name = (char*)malloc(strlen(output_file_name)+35); char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
@@ -12723,7 +12727,7 @@ long long gap_fuzz, bub_label_t* b_mask_t)
ug = ma_ug_gen_primary(sg, PRIMARY_LABLE); ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
new_rtg_edges.a.n = 0; new_rtg_edges.a.n = 0;
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, &d_edges);///polish ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, &d_edges, 1);///polish
hap_cov_t *cov = NULL; hap_cov_t *cov = NULL;
@@ -12763,7 +12767,7 @@ long long gap_fuzz, bub_label_t* b_mask_t)
} }
char* gfa_name = (char*)malloc(strlen(output_file_name)+25); char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.clean_d_utg.noseq.gfa", output_file_name); sprintf(gfa_name, "%s.pre.clean_d_utg.noseq.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w"); FILE* output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, sg, coverage_cut, sources, ruIndex, "utg", output_file); ma_ug_print_simple(ug, &R_INF, sg, coverage_cut, sources, ruIndex, "utg", output_file);
fclose(output_file); fclose(output_file);
@@ -12774,6 +12778,14 @@ long long gap_fuzz, bub_label_t* b_mask_t)
if(cov) destory_hap_cov_t(&cov); if(cov) destory_hap_cov_t(&cov);
if(t_ch) destory_trans_chain(&t_ch); if(t_ch) destory_trans_chain(&t_ch);
gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.after.clean_d_utg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, sg, coverage_cut, sources, ruIndex, "utg", output_file);
fclose(output_file);
free(gfa_name);
ma_ug_destroy(ug); ma_ug_destroy(ug);
kv_destroy(new_rtg_edges.a); kv_destroy(new_rtg_edges.a);
@@ -13752,7 +13764,7 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
} }
} }
ma_ug_seq(ug, read_g, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0); ma_ug_seq(ug, read_g, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
fprintf(stderr, "Writing raw unitig GFA to disk... \n"); fprintf(stderr, "Writing raw unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+25); char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
@@ -16160,7 +16172,7 @@ float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench,
///debug_utg_graph(ug, sg, 0, 0); ///debug_utg_graph(ug, sg, 0, 0);
///debug_untig_length(ug, tipsLen, gfa_name); ///debug_untig_length(ug, tipsLen, gfa_name);
///print_untig_by_read(ug, "m64011_190901_095311/125831121/ccs", 2310925, "end"); ///print_untig_by_read(ug, "m64011_190901_095311/125831121/ccs", 2310925, "end");
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0); ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
if(is_bench) if(is_bench)
{ {
free(gfa_name); free(gfa_name);
@@ -18831,24 +18843,6 @@ long long asg_arc_del_simple_circle_untig(ma_hit_t_alloc* sources, ma_sub_t* cov
} }
uint32_t* build_unitig_index(asg_t *sg, ma_ug_t *ug)
{
if(sg == NULL && ug == NULL) return NULL;
uint32_t* index = (uint32_t*)calloc(sg->n_seq, sizeof(uint32_t));
uint32_t i, j;
for (i = 0; i < ug->u.n; ++i)
{
ma_utg_t *u = &(ug->u.a[i]);
for (j = 0; j < u->n; j++)
{
index[(u->a[j]>>33)] = i;
}
}
return index;
}
int double_check_tangle(uint32_t vBeg, uint32_t vEnd, uint32_t* u_vecs, uint32_t n, asg_t *nsg) int double_check_tangle(uint32_t vBeg, uint32_t vEnd, uint32_t* u_vecs, uint32_t n, asg_t *nsg)
{ {
uint32_t v, nv, k, i, j; uint32_t v, nv, k, i, j;
@@ -24049,7 +24043,7 @@ R_to_U* ruIndex, int max_hang, int min_ovlp)
} }
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0); ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
fprintf(stderr, "Writing processed unitig GFA to disk... \n"); fprintf(stderr, "Writing processed unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+35); char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
@@ -24100,7 +24094,7 @@ R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ov
break_ug_contig(&ug, sg, &R_INF, coverage_cut, sources, ruIndex, &new_rtg_edges, max_hang, min_ovlp, break_ug_contig(&ug, sg, &R_INF, coverage_cut, sources, ruIndex, &new_rtg_edges, max_hang, min_ovlp,
NULL, &asm_opt.b_high_cov, asm_opt.m_rate); NULL, &asm_opt.b_high_cov, asm_opt.m_rate);
} }
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0); ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
fprintf(stderr, "Writing primary contig GFA to disk... \n"); fprintf(stderr, "Writing primary contig GFA to disk... \n");
@@ -24144,7 +24138,7 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
// break_ug_contig(&ug, sg, &R_INF, coverage_cut, sources, ruIndex, &new_rtg_edges, max_hang, min_ovlp, asm_opt.b_low_cov); // break_ug_contig(&ug, sg, &R_INF, coverage_cut, sources, ruIndex, &new_rtg_edges, max_hang, min_ovlp, asm_opt.b_low_cov);
// } // }
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0); ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
fprintf(stderr, "Writing alternate contig GFA to disk... \n"); fprintf(stderr, "Writing alternate contig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+35); char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
Overlaps.h
+2
View File
@@ -1192,6 +1192,8 @@ ma_ug_t *ug, uint32_t flag, double overall_score, const char* cmd);
int asg_arc_del_trans(asg_t *g, int fuzz); int asg_arc_del_trans(asg_t *g, int fuzz);
void kt_u_trans_t_idx(kv_u_trans_t *ta, uint32_t n); void kt_u_trans_t_idx(kv_u_trans_t *ta, uint32_t n);
uint32_t get_u_trans_spec(kv_u_trans_t *ta, uint32_t qn, uint32_t tn, u_trans_t **r_a, uint32_t *occ); uint32_t get_u_trans_spec(kv_u_trans_t *ta, uint32_t qn, uint32_t tn, u_trans_t **r_a, uint32_t *occ);
int ma_ug_seq(ma_ug_t *g, asg_t *read_g, ma_sub_t *coverage_cut, ma_hit_t_alloc* sources,
kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp, kvec_asg_arc_t_warp *E, uint32_t is_polish);
#define JUNK_COV 5 #define JUNK_COV 5
#define DISCARD_RATE 0.8 #define DISCARD_RATE 0.8
Purge_Dups.cpp
+39 -7
View File
@@ -2242,10 +2242,10 @@ uint32_t* xBeg, uint32_t* xEnd, uint32_t* yBeg, uint32_t* yEnd)
KRADIX_SORT_INIT(i32, int32_t, generic_key, sizeof(int32_t)) KRADIX_SORT_INIT(i32, int32_t, generic_key, sizeof(int32_t))
long long get_chain_score(ma_utg_t *xReads, asg_t *read_g, kvec_asg_arc_t_offset* u_buffer, kvec_t_i32_warp* tailIndex, kvec_t_i32_warp* idx, long long get_chain_score(ma_utg_t *xReads, asg_t *read_g, kvec_asg_arc_t_offset* u_buffer, kvec_t_i32_warp* tailIndex, kvec_t_i32_warp* idx,
ma_hit_t_alloc* reverse_sources, long long xBegPos, long long xEndPos) ma_hit_t_alloc* reverse_sources, long long xBegPos, long long xEndPos, uint32_t xUid, uint32_t yUid)
{ {
long long offset, r_beg, r_end, inp_beg, inp_end, hap_beg, hap_end, inp_match, hap_match, ovlp; long long offset, r_beg, r_end, inp_beg, inp_end, hap_beg, hap_end, inp_match, hap_match, ovlp;
uint64_t i, k, rId; uint64_t i, k, rId, all, found;
idx->a.n = 0; idx->a.n = 0;
for (i = k = 0; i < tailIndex->a.n; i++) for (i = k = 0; i < tailIndex->a.n; i++)
@@ -2331,8 +2331,19 @@ ma_hit_t_alloc* reverse_sources, long long xBegPos, long long xEndPos)
// if(inp_match > hap_match) fprintf(stderr, "ERROR3\n"); // if(inp_match > hap_match) fprintf(stderr, "ERROR3\n");
// fprintf(stderr, "tailIndex->a.n: %u, xReads->n: %u, total_match: %lld, hap_match: %lld, inp_match: %lld\n", // fprintf(stderr, "tailIndex->a.n: %u, xReads->n: %u, total_match: %lld, hap_match: %lld, inp_match: %lld\n",
// tailIndex->a.n, xReads->n, (xEndPos - xBegPos + 1), hap_match, inp_match); // tailIndex->a.n, xReads->n, (xEndPos - xBegPos + 1), hap_match, inp_match);
double base_w = 0, k_w = 1;
return ((double)(inp_match)*CHAIN_MATCH) - ((double)(hap_match-inp_match)*CHAIN_UNMATCH); base_w = ((double)(inp_match)*CHAIN_MATCH) - ((double)(hap_match-inp_match)*CHAIN_UNMATCH);
if(base_w <= 0) return base_w; ///hard filter
if(!count_unique_k_mers(xReads->s + xBegPos, xEndPos+1-xBegPos, xUid, yUid, &all, &found))
{
return base_w;
}
if(all > 0) k_w += ((double)(found)/(double)(all));
return (base_w*k_w)/2;
// return ((double)(inp_match)*CHAIN_MATCH) - ((double)(hap_match-inp_match)*CHAIN_UNMATCH);
} }
@@ -2378,7 +2389,7 @@ kvec_t_i32_warp* prevIndex, long long* r_x_pos_beg, long long* r_x_pos_end, long
hap_can->weight = xLeftMatch; hap_can->weight = xLeftMatch;
hap_can->index_beg = xLeftTotal; hap_can->index_beg = xLeftTotal;
hap_can->score = get_chain_score(xReads, read_g, u_buffer, tailIndex, prevIndex, reverse_sources, hap_can->score = get_chain_score(xReads, read_g, u_buffer, tailIndex, prevIndex, reverse_sources,
(*r_x_pos_beg), (*r_x_pos_end)); (*r_x_pos_beg), (*r_x_pos_end), xUid, yUid);
if(hap_can->score <= 0) return (uint32_t)-1; if(hap_can->score <= 0) return (uint32_t)-1;
return hap_can->index_end; return hap_can->index_end;
} }
@@ -2541,7 +2552,14 @@ long long* r_y_pos_beg, long long* r_y_pos_end, float *sim)
(*sim) = ((double)xLeftMatch)/((double)xLeftTotal); (*sim) = ((double)xLeftMatch)/((double)xLeftTotal);
if(xLeftMatch == 0 || xLeftTotal == 0 || xLeftMatch <= xLeftTotal*Hap_rate) if(xLeftMatch == 0 || xLeftTotal == 0 || xLeftMatch <= xLeftTotal*Hap_rate)
{ {
return NON_PLOID; uint64_t all, found;
if(!count_unique_k_mers(xReads->s + (*r_x_pos_beg), (*r_x_pos_end)+1-(*r_x_pos_beg),
xUid, yUid, &all, &found))
{
return NON_PLOID;
}
(*sim) = MAX((*sim), (((double)found)/((double)all)));
if(found == 0 || all == 0 || found <= all*Hap_rate) return NON_PLOID;
} }
return PLOID; return PLOID;
@@ -5263,7 +5281,12 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans, uint32_t colle
} }
} }
if(just_coverage == 0)
{
ma_ug_seq(ug, read_g, coverage_cut, sources, edge, max_hang, min_ovlp, 0, 0);
}
init_ug_idx(ug, asm_opt.k_mer_length, asm_opt.polyploidy, 2, !just_coverage);
init_hap_alignment_struct_pip(&hap_buf, asm_opt.thread_num, nsg->n_seq, ug, read_g, init_hap_alignment_struct_pip(&hap_buf, asm_opt.thread_num, nsg->n_seq, ug, read_g,
sources, reverse_sources, ruIndex, coverage_cut, position_index, density, max_hang, min_ovlp, sources, reverse_sources, ruIndex, coverage_cut, position_index, density, max_hang, min_ovlp,
0.1, &all_ovlp, cov); 0.1, &all_ovlp, cov);
@@ -5392,4 +5415,13 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans, uint32_t colle
else free(position_index); else free(position_index);
destory_hap_alignment_struct_pip(&hap_buf); destory_hap_alignment_struct_pip(&hap_buf);
destory_p_g_t(&pg); destory_p_g_t(&pg);
if(just_coverage == 0)
{
des_ug_idx();
for (i = 0; i < ug->u.n; i++)
{
free(ug->u.a[i].s);
ug->u.a[i].s = NULL;
}
}
} }
hic.cpp
+92 -27
View File
@@ -153,7 +153,7 @@ typedef struct {
uint64_t pre; uint64_t pre;
uint64_t tot; uint64_t tot;
uint64_t tot_pos; uint64_t tot_pos;
uint64_t up_bound; uint64_t up_bound, low_bound;
hc_pt1_t* idx_buf; hc_pt1_t* idx_buf;
long double a, b, frac, max_d; long double a, b, frac, max_d;
} ha_ug_index; } ha_ug_index;
@@ -310,7 +310,8 @@ void print_debug_bubble_graph(bubble_type* bub, ma_ug_t* ug, const char *fn);
void build_bub_graph(ma_ug_t* ug, bubble_type* bub); void build_bub_graph(ma_ug_t* ug, bubble_type* bub);
void init_ha_ug_index_opt(ha_ug_index* idx, ma_ug_t *ug, int k, pldat_t* p) void init_ha_ug_index_opt(ha_ug_index* idx, ma_ug_t *ug, int k, pldat_t* p, uint64_t up_occ,
uint64_t low_occ, uint64_t thread_num)
{ {
uint64_t i, n; uint64_t i, n;
for (idx->uID_bits=1; (uint64_t)(1<<idx->uID_bits)<(uint64_t)ug->u.n; idx->uID_bits++); for (idx->uID_bits=1; (uint64_t)(1<<idx->uID_bits)<(uint64_t)ug->u.n; idx->uID_bits++);
@@ -324,7 +325,8 @@ void init_ha_ug_index_opt(ha_ug_index* idx, ma_ug_t *ug, int k, pldat_t* p)
idx->tot = 1 << idx->pre; idx->tot = 1 << idx->pre;
idx->tot_pos = 0; idx->tot_pos = 0;
///idx->up_bound = 1; ///idx->up_bound = 1;
idx->up_bound = asm_opt.hap_occ; idx->up_bound = up_occ;
idx->low_bound = low_occ;
CALLOC(idx->idx_buf, idx->tot); CALLOC(idx->idx_buf, idx->tot);
for (i = 0; i < idx->tot; i++) for (i = 0; i < idx->tot; i++)
{ {
@@ -344,7 +346,7 @@ void init_ha_ug_index_opt(ha_ug_index* idx, ma_ug_t *ug, int k, pldat_t* p)
kv_init(p->cnt[i].a); kv_init(p->cnt[i].a);
kv_init(p->buf[i].a); kv_init(p->buf[i].a);
} }
p->n_thread = asm_opt.thread_num; p->n_thread = thread_num;
} }
inline uint64_t get_k_direction(uint64_t x[4]) inline uint64_t get_k_direction(uint64_t x[4])
@@ -463,16 +465,17 @@ void test_unitig_index(ha_ug_index* idx, ma_ug_t *ug)
fprintf(stderr, "[M::%s::%.3f] ==> Test has been passed\n", __func__, yak_realtime()-index_time); fprintf(stderr, "[M::%s::%.3f] ==> Test has been passed\n", __func__, yak_realtime()-index_time);
} }
void hc_pt_t_gen_single(hc_pt1_t* pt, uint64_t* up_bound) void hc_pt_t_gen_single(hc_pt1_t* pt, uint64_t* up_bound, uint64_t* low_bound)
{ {
khint_t k; khint_t k;
uint64_t c; uint64_t c;
if(up_bound) if(up_bound || low_bound)
{ {
for (k = 0; k != kh_end(pt->h); ++k) { for (k = 0; k != kh_end(pt->h); ++k) {
if (kh_exist(pt->h, k)) { if (kh_exist(pt->h, k)) {
if(kh_val(pt->h, k) > (*up_bound)) if((up_bound && kh_val(pt->h, k) > (*up_bound)) ||
(low_bound && kh_val(pt->h, k) < (*low_bound)))
{ {
kh_val(pt->h, k) = 0; kh_val(pt->h, k) = 0;
kh_key(pt->h, k) = (kh_key(pt->h, k)&HIC_KEY_MODE)| kh_key(pt->h, k) = (kh_key(pt->h, k)&HIC_KEY_MODE)|
@@ -614,7 +617,7 @@ void hc_pt_t_gen(ha_ug_index* idx, pldat_t* pl)
uint64_t i; uint64_t i;
for (i = 0; i < idx->tot; i++) for (i = 0; i < idx->tot; i++)
{ {
hc_pt_t_gen_single(&(idx->idx_buf[i]), &(idx->up_bound)); hc_pt_t_gen_single(&(idx->idx_buf[i]), &(idx->up_bound), &(idx->low_bound));
} }
} }
else else
@@ -785,12 +788,12 @@ void parallel_count_hc_pt1(pldat_t* pl)
} }
} }
ha_ug_index* build_unitig_index(ma_ug_t *ug, int k) ha_ug_index* build_unitig_index(ma_ug_t *ug, int k, uint64_t up_occ, uint64_t low_occ, uint64_t thread_num)
{ {
ha_ug_index* idx = NULL; CALLOC(idx, 1); ha_ug_index* idx = NULL; CALLOC(idx, 1);
pldat_t pl; pl.h = idx; pl.is_cnt = 1; pldat_t pl; pl.h = idx; pl.is_cnt = 1;
double index_time = yak_realtime(), beg_time; double index_time = yak_realtime(), beg_time;
init_ha_ug_index_opt(idx, ug, k, &pl); init_ha_ug_index_opt(idx, ug, k, &pl, up_occ, low_occ, thread_num);
beg_time = yak_realtime(); beg_time = yak_realtime();
pl.is_cnt = 1; pl.is_cnt = 1;
@@ -15250,7 +15253,7 @@ void verbose_het_stat(bubble_type *bub)
fprintf(stderr, "[M::stat] # heterozygous bases: %lu; # homozygous bases: %lu\n", hetBase, homBase); fprintf(stderr, "[M::stat] # heterozygous bases: %lu; # homozygous bases: %lu\n", hetBase, homBase);
} }
void debug_output_disconnected_hits(ha_ug_index* idx, kvec_pe_hit *hits, hc_links *link, bubble_type *bub) void debug_output_disconnected_hits(ha_ug_index* idx, kv_u_trans_t *ta, kvec_pe_hit *hits, hc_links *link, bubble_type *bub, int8_t *s)
{ {
uint32_t k, l, i, m, h_occ; uint32_t k, l, i, m, h_occ;
uint64_t shif = 64 - idx->uID_bits, qn, tn, u_dis; uint64_t shif = 64 - idx->uID_bits, qn, tn, u_dis;
@@ -15328,22 +15331,26 @@ void debug_output_disconnected_hits(ha_ug_index* idx, kvec_pe_hit *hits, hc_link
u_dis = (t->e.a[k].dis ==(uint64_t)-1? (uint64_t)-1 : t->e.a[k].dis>>3); u_dis = (t->e.a[k].dis ==(uint64_t)-1? (uint64_t)-1 : t->e.a[k].dis>>3);
break; break;
} }
get_u_trans_spec(ta, qn, tn, &p, NULL);
fprintf(stderr, "s-utg%.6lul<--->d-utg%.6lul(occ: %u):(dis-%lu)\n", qn + 1, tn + 1, fprintf(stderr, "s-utg%.6lul[hap-%d]<--->d-utg%.6lul[hap-%d](occ: %u, ",
((uint32_t)-1) - k_trans.a[i].occ, u_dis); qn + 1, s[qn], tn + 1, s[tn], ((uint32_t)-1) - k_trans.a[i].occ);
if(p) fprintf(stderr, "weight: %f", p->nw);
else fprintf(stderr, "weight: NA");
fprintf(stderr, "):(dis-%lu)\n", u_dis);
} }
fprintf(stderr, "########hits########\n"); // fprintf(stderr, "########hits########\n");
char dir[2] = {'+', '-'}; // char dir[2] = {'+', '-'};
for (k = 0; k < hits->a.n; ++k) // for (k = 0; k < hits->a.n; ++k)
{ // {
fprintf(stderr, "%c\tutg%.6dl(len-%u)\t%lu\t%c\tutg%.6dl(len-%u)\t%lu\ti:%lu\n", // fprintf(stderr, "%c\tutg%.6dl(len-%u)\t%lu\t%c\tutg%.6dl(len-%u)\t%lu\ti:%lu\n",
dir[hits->a.a[k].s>>63], (int)((hits->a.a[k].s<<1)>>shif)+1, // dir[hits->a.a[k].s>>63], (int)((hits->a.a[k].s<<1)>>shif)+1,
idx->ug->g->seq[((hits->a.a[k].s<<1)>>shif)].len, hits->a.a[k].s&idx->pos_mode, // idx->ug->g->seq[((hits->a.a[k].s<<1)>>shif)].len, hits->a.a[k].s&idx->pos_mode,
dir[hits->a.a[k].e>>63], (int)((hits->a.a[k].e<<1)>>shif)+1, // dir[hits->a.a[k].e>>63], (int)((hits->a.a[k].e<<1)>>shif)+1,
idx->ug->g->seq[((hits->a.a[k].e<<1)>>shif)].len, hits->a.a[k].e&idx->pos_mode, // idx->ug->g->seq[((hits->a.a[k].e<<1)>>shif)].len, hits->a.a[k].e&idx->pos_mode,
hits->a.a[k].id); // hits->a.a[k].id);
} // }
kv_destroy(k_trans); kv_destroy(k_trans);
} }
@@ -15482,7 +15489,7 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
/*******************************for debug************************************/ /*******************************for debug************************************/
// if(bub.round_id == bub.n_round - 1) // if(bub.round_id == bub.n_round - 1)
// { // {
// debug_output_disconnected_hits(idx, &sl.hits, &link, &bub); // debug_output_disconnected_hits(idx, &k_trans, &sl.hits, &link, &bub, s->s);
// } // }
/*******************************for debug************************************/ /*******************************for debug************************************/
/** /**
@@ -15540,7 +15547,7 @@ void hic_analysis(ma_ug_t *ug, asg_t* read_g, trans_chain* t_ch)
ug_index = NULL; ug_index = NULL;
int exist = (asm_opt.load_index_from_disk? int exist = (asm_opt.load_index_from_disk?
load_hc_pt_index(&ug_index, asm_opt.output_file_name) : 0); load_hc_pt_index(&ug_index, asm_opt.output_file_name) : 0);
if(exist == 0) ug_index = build_unitig_index(ug, asm_opt.hic_mer_length); if(exist == 0) ug_index = build_unitig_index(ug, asm_opt.hic_mer_length, asm_opt.hap_occ, 0, asm_opt.thread_num);
if(exist == 0) write_hc_pt_index(ug_index, asm_opt.output_file_name); if(exist == 0) write_hc_pt_index(ug_index, asm_opt.output_file_name);
ug_index->ug = ug; ug_index->ug = ug;
ug_index->read_g = read_g; ug_index->read_g = read_g;
@@ -15551,6 +15558,64 @@ void hic_analysis(ma_ug_t *ug, asg_t* read_g, trans_chain* t_ch)
destory_hc_pt_index(ug_index); destory_hc_pt_index(ug_index);
} }
void init_ug_idx(ma_ug_t *ug, uint64_t k, uint64_t up_bound, uint64_t low_bound, uint64_t build_idx)
{
ug_index = NULL;
if(build_idx)
{
ug_index = build_unitig_index(ug, k, up_bound, low_bound, asm_opt.thread_num);
}
}
void des_ug_idx()
{
destory_hc_pt_index(ug_index);
}
uint64_t count_unique_k_mers(char *r, uint64_t len, uint64_t query, uint64_t target, uint64_t *all, uint64_t *found)
{
if(!ug_index) return 0;
uint64_t i, j, l = 0, skip, *pos_list = NULL, cnt, uID, is_q, k_mer = ug_index->k;
uint64_t x[4], mask = (1ULL<<k_mer) - 1, shift = k_mer - 1, hash;
(*all) = (*found) = 0;
for (i = l = 0, x[0] = x[1] = x[2] = x[3] = 0; i < len; ++i) {
int c = seq_nt4_table[(uint8_t)r[i]];
///c = 00, 01, 10, 11
if (c < 4) { // not an "N" base
///x[0] & x[1] are the forward k-mer
///x[2] & x[3] are the reverse complementary k-mer
x[0] = (x[0] << 1 | (c&1)) & mask;
x[1] = (x[1] << 1 | (c>>1)) & mask;
x[2] = x[2] >> 1 | (uint64_t)(1 - (c&1)) << shift;
x[3] = x[3] >> 1 | (uint64_t)(1 - (c>>1)) << shift;
if (++l >= k_mer)
{
hash = hc_hash_long(x, &skip, k_mer);
if(skip == (uint64_t)-1) continue;
cnt = get_hc_pt1_count((ha_ug_index*)ug_index, hash, &pos_list);
if(cnt <= 0) continue;
for (j = 0, is_q = 0; j < cnt; j++)
{
uID = (pos_list[j] << 1) >> (64 - ug_index->uID_bits);
if(query == uID) is_q = 1;
if(target == uID) break;
}
if(is_q)
{
(*found)++;
if(j < cnt) (*all)++;
}
}
} else l = 0, x[0] = x[1] = x[2] = x[3] = 0; // if there is an "N", restart
}
return 1;
}
typedef struct{ typedef struct{
//[uID_start, uID_end) //[uID_start, uID_end)
uint64_t uID_start; uint64_t uID_start;
@@ -15958,7 +16023,7 @@ void hic_benchmark(ma_ug_t *ug, asg_t* read_g)
sprintf(output_file_name, "%s.bench", asm_opt.output_file_name); sprintf(output_file_name, "%s.bench", asm_opt.output_file_name);
ug_index = NULL; ug_index = NULL;
int exist = load_hc_pt_index(&ug_index, output_file_name); int exist = load_hc_pt_index(&ug_index, output_file_name);
if(exist == 0) ug_index = build_unitig_index(ug, asm_opt.hic_mer_length); if(exist == 0) ug_index = build_unitig_index(ug, asm_opt.hic_mer_length, asm_opt.hap_occ, 0, asm_opt.thread_num);
if(exist == 0) write_hc_pt_index(ug_index, output_file_name); if(exist == 0) write_hc_pt_index(ug_index, output_file_name);
ug_index->ug = ug; ug_index->ug = ug;
ug_index->read_g = read_g; ug_index->read_g = read_g;
hic.h
+3
View File
@@ -74,5 +74,8 @@ void get_bub_id(bubble_type* bub, uint32_t root, uint64_t* id0, uint64_t* id1, u
void update_bubble_chain(ma_ug_t* ug, bubble_type* bub, uint32_t is_middle, uint32_t is_end); void update_bubble_chain(ma_ug_t* ug, bubble_type* bub, uint32_t is_middle, uint32_t is_end);
void set_b_utg_weight_flag(bubble_type* bub, buf_t* b, uint32_t v, uint8_t* vis_flag, uint32_t flag, uint32_t* occ); void set_b_utg_weight_flag(bubble_type* bub, buf_t* b, uint32_t v, uint8_t* vis_flag, uint32_t flag, uint32_t* occ);
void debug_gfa_space(ma_ug_t* ug, hap_cov_t *cov); void debug_gfa_space(ma_ug_t* ug, hap_cov_t *cov);
void init_ug_idx(ma_ug_t *ug, uint64_t k, uint64_t up_bound, uint64_t low_bound, uint64_t build_idx);
void des_ug_idx();
uint64_t count_unique_k_mers(char *r, uint64_t len, uint64_t query, uint64_t target, uint64_t *all, uint64_t *found);
#endif #endif