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chhylp123
2021-03-14 03:25:19 -04:00
parent 4c2ce6fc6b
commit 8e4b98f0a6
5 changed files with 1161 additions and 406 deletions
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Overlaps.h
+40 -65
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@@ -551,55 +551,6 @@ inline uint32_t check_tip(asg_t *sg, uint32_t begNode, uint32_t* endNode, buf_t*
}
}
inline uint32_t get_unitig_back(asg_t *sg, ma_ug_t *ug, uint32_t begNode, uint32_t* endNode,
long long* nodeLen, long long* baseLen, buf_t* b)
{
ma_utg_v* u = NULL;
uint32_t v = begNode, w, k;
uint32_t kv;
(*nodeLen) = (*baseLen) = 0;
(*endNode) = (uint32_t)-1;
if(ug!=NULL) u = &(ug->u);
while (1)
{
kv = get_real_length(sg, v, NULL);
(*endNode) = v;
if(u == NULL)
{
(*nodeLen)++;
}
else
{
(*nodeLen) += EvaluateLen((*u), v>>1);
}
if(b) kv_push(uint32_t, b->b, v);
///means reach the end of a unitig
if(kv!=1) (*baseLen) += sg->seq[v>>1].len;
if(kv==0) return END_TIPS;
if(kv>1) return MUL_OUTPUT;
///kv must be 1 here
kv = get_real_length(sg, v, &w);
///means reach the end of a unitig
if(get_real_length(sg, w^1, NULL)!=1)
{
(*baseLen) += sg->seq[v>>1].len;
return MUL_INPUT;
}
for (k = 0; k < asg_arc_n(sg, v); k++)
{
if(asg_arc_a(sg, v)[k].del) continue;
///here is just one undeleted edge
(*baseLen) += asg_arc_len(asg_arc_a(sg, v)[k]);
break;
}
v = w;
if(v == begNode) return LOOP;
}
}
inline uint32_t get_unitig(asg_t *sg, ma_ug_t *ug, uint32_t begNode, uint32_t* endNode,
long long* nodeLen, long long* baseLen, long long* max_stop_nodeLen, long long* max_stop_baseLen,
uint32_t stops_threshold, buf_t* b)
@@ -1030,25 +981,47 @@ typedef struct {
uint32_t total;
} Trio_counter;
typedef struct {
uint32_t p; // the optimal parent vertex
uint32_t d; // the shortest distance from the initial vertex
uint32_t r:31, s:1; // r: the number of remaining incoming arc; s: state
} binfo_s_t;
typedef struct {
///all information for each node
binfo_s_t *a;
kvec_t(uint32_t) S; // set of vertices without parents, nodes with all incoming edges visited
kvec_t(uint32_t) b; // visited vertices
kvec_t(uint32_t) e; // visited edges/arcs
} buf_s_t;
typedef struct{
buf_s_t *b;
uint32_t n_thres, n_reads;
asg_t *g;
uint32_t check_cross;
uint64_t bub_dist;
} bub_label_t;
void resolve_tangles(ma_ug_t *src, asg_t *read_g, ma_hit_t_alloc* reverse_sources, long long minLongUntig,
long long maxShortUntig, float l_untig_rate, float max_node_threshold, R_to_U* ruIndex, uint32_t trio_flag,
float drop_ratio);
void adjust_utg_advance(asg_t *sg, ma_ug_t *ug, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex);
void rescue_contained_reads_aggressive(ma_ug_t *i_ug, asg_t *r_g, ma_hit_t_alloc* sources, ma_sub_t *coverage_cut,
R_to_U* ruIndex, int max_hang, int min_ovlp, long long bubble_dist, uint32_t chainLenThres, uint32_t is_bubble_check,
uint32_t is_primary_check, kvec_asg_arc_t_warp* new_rtg_edges, kvec_t_u32_warp* new_rtg_nodes);
uint32_t is_primary_check, kvec_asg_arc_t_warp* new_rtg_edges, kvec_t_u32_warp* new_rtg_nodes, bub_label_t* b_mask_t);
void rescue_missing_overlaps_aggressive(ma_ug_t *i_ug, asg_t *r_g, ma_hit_t_alloc* sources, ma_sub_t *coverage_cut,
R_to_U* ruIndex, int max_hang, int min_ovlp, long long bubble_dist, uint32_t is_bubble_check,
uint32_t is_primary_check, kvec_asg_arc_t_warp* new_rtg_edges);
uint32_t is_primary_check, kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t);
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, float double_check_rate);
void drop_semi_circle(ma_ug_t *ug, asg_t* nsg, asg_t* read_g, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex);
void rescue_wrong_overlaps_to_unitigs(ma_ug_t *i_ug, asg_t *r_g, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
ma_sub_t *coverage_cut, R_to_U* ruIndex, int max_hang, int min_ovlp, long long bubble_dist, kvec_asg_arc_t_warp* keep_edges);
ma_sub_t *coverage_cut, R_to_U* ruIndex, int max_hang, int min_ovlp, long long bubble_dist, kvec_asg_arc_t_warp* keep_edges, bub_label_t* b_mask_t);
void get_unitig_trio_flag(ma_utg_t* nsu, uint32_t flag, uint32_t* require, uint32_t* non_require, uint32_t* ambigious);
void rescue_missing_overlaps_backward(ma_ug_t *i_ug, asg_t *r_g, ma_hit_t_alloc* sources, ma_sub_t *coverage_cut,
R_to_U* ruIndex, int max_hang, int min_ovlp, long long bubble_dist, uint32_t backward_steps,
uint32_t is_bubble_check, uint32_t is_primary_check);
uint32_t is_bubble_check, uint32_t is_primary_check, bub_label_t* b_mask_t);
uint32_t get_edge_from_source(ma_hit_t_alloc* sources, ma_sub_t *coverage_cut,
R_to_U* ruIndex, int max_hang, int min_ovlp, uint32_t query, uint32_t target, asg_arc_t* t);
int unitig_arc_del_short_diploid_by_length(asg_t *g, float drop_ratio);
@@ -1085,12 +1058,15 @@ typedef struct{
uint64_t r_num;
} hc_links;
typedef struct{
kvec_t(uint32_t) uIDs;
kvec_t(uint32_t) idx;
uint32_t chain_num;
kvec_t(uint32_t) iDXs;
kvec_t(uint32_t) rescue_hom;
uint32_t* u_idx;
uint64_t r_num;
uint32_t r_num;
uint32_t chain_num;
uint32_t l0_chain, l1_chain;
}trans_chain;
typedef struct {
@@ -1106,8 +1082,8 @@ typedef struct {
kvec_asg_arc_t_offset u_buffer;
kvec_t_i32_warp tailIndex;
kvec_t_i32_warp prevIndex;
hc_links* link;
///trans_chain t_ch;
///hc_links* link;
trans_chain* t_ch;
}hap_cov_t;
typedef struct{
@@ -1118,28 +1094,27 @@ typedef struct{
void init_hc_links(hc_links* link, uint64_t ug_num, uint64_t r_num);
void destory_hc_links(hc_links* link);
int asg_pop_bubble_primary_trio(ma_ug_t *ug, int max_dist, uint32_t positive_flag, uint32_t negative_flag, hap_cov_t *cov);
uint64_t asg_bub_pop1_primary_trio(asg_t *g, ma_ug_t *utg, uint32_t v0, int max_dist, buf_t *b, uint32_t positive_flag,
uint64_t get_bub_pop_max_dist(asg_t *g, buf_t *b);
uint64_t get_bub_pop_max_dist_advance(asg_t *g, buf_t *b);
int asg_pop_bubble_primary_trio(ma_ug_t *ug, uint64_t* i_max_dist, uint32_t positive_flag, uint32_t negative_flag, hap_cov_t *cov);
uint64_t asg_bub_pop1_primary_trio(asg_t *g, ma_ug_t *utg, uint32_t v0, uint64_t max_dist, buf_t *b, uint32_t positive_flag,
uint32_t negative_flag, uint32_t is_pop, uint64_t* path_base_len, uint64_t* path_nodes, hap_cov_t *cov);
void adjust_utg_by_primary(ma_ug_t **ug, asg_t* read_g, float drop_rate,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, ma_sub_t* coverage_cut,
long long bubble_dist, long long tipsLen, float tip_drop_ratio, long long stops_threshold,
R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp,
kvec_asg_arc_t_warp* new_rtg_edges, hc_links* link);
kvec_asg_arc_t_warp* new_rtg_edges, hc_links* link, bub_label_t* b_mask_t);
void collect_reverse_unitigs(buf_t* b_0, buf_t* b_1, hc_links* link, ma_ug_t *ug, asg_t *read_sg);
ma_ug_t* copy_untig_graph(ma_ug_t *src);
ma_ug_t* output_trio_unitig_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
uint8_t flag, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, long long bubble_dist,
long long tipsLen, float tip_drop_ratio, long long stops_threshold, R_to_U* ruIndex,
float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench);
float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench, bub_label_t* b_mask_t);
asg_t* copy_read_graph(asg_t *src);
ma_ug_t *ma_ug_gen(asg_t *g);
void ma_ug_destroy(ma_ug_t *ug);
inline int inter_interval(int a_s, int a_e, int b_s, int b_e, int* i_s, int* i_e)
{
if(a_s > b_e || b_s > a_e) return 0;