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init partition

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chhylp123
2020-12-26 19:01:24 -05:00
parent f3e390eee8
commit 53a655d802
7 changed files with 1887 additions and 183 deletions
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Overlaps.h
+11 -12
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@@ -155,6 +155,7 @@ typedef struct { size_t n, m; ma_utg_t *a; } ma_utg_v;
typedef struct {
ma_utg_v u;
asg_t *g;
kvec_t(uint64_t) occ;
} ma_ug_t;
typedef struct {
@@ -743,13 +744,12 @@ R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
stops_threshold, b_0) == LOOP)
{
return UNAVAILABLE;
}
}
if(get_unitig(nsg, ug, v_1, &vEnd, &ELen_1, &tmp, &max_stop_nodeLen, &max_stop_baseLen,
stops_threshold, b_1) == LOOP)
{
return UNAVAILABLE;
}
if(ELen_0<=min_edge_length || ELen_1<=min_edge_length) return UNAVAILABLE;
rIdContig b_max, b_min;
@@ -770,7 +770,6 @@ R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
uint32_t max_count = 0, min_count = 0;
ma_utg_t *node_min = NULL, *node_max = NULL;
if(ug != NULL)
{
/*****************************label all unitigs****************************************/
@@ -786,7 +785,6 @@ R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
}
/*****************************label all unitigs****************************************/
///each unitig
for (b_min.untigI = 0; b_min.untigI < b_min.b_0->b.n; b_min.untigI++)
{
@@ -820,7 +818,6 @@ R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
}
}
}
/*****************************label all unitigs****************************************/
for (b_max.untigI = 0; b_max.untigI < b_max.b_0->b.n; b_max.untigI++)
{
@@ -833,7 +830,6 @@ R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
}
}
/*****************************label all unitigs****************************************/
}
else
{
@@ -896,8 +892,6 @@ R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
return NON_PLOID;
}
inline uint32_t check_different_haps_naive(asg_t *nsg, ma_ug_t *ug, asg_t *read_sg,
uint32_t v_0, uint32_t v_1, ma_hit_t_alloc* reverse_sources, buf_t* b_0, buf_t* b_1,
R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
@@ -1061,7 +1055,7 @@ uint32_t is_bubble_check, uint32_t is_primary_check);
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);
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, uint32_t negative_flag, uint32_t is_pop);
uint32_t positive_flag, uint32_t negative_flag, uint32_t is_pop, uint64_t* path_base_len);
int unitig_arc_del_short_diploid_by_length(asg_t *g, float drop_ratio);
@@ -1089,7 +1083,8 @@ typedef struct{
hc_edge *a;
}hc_edge_warp;
void init_hc_links(hc_links* link, uint64_t ug_num, uint64_t r_num);
void destory_hc_links(hc_links* link);
void clean_primary_untig_graph(ma_ug_t *ug, asg_t *read_g, 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, buf_t* b_0, uint8_t* visit, float density, uint32_t miniHapLen,
@@ -1100,8 +1095,12 @@ 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);
void collect_reverse_unitigs(buf_t* b_0, buf_t* b_1, hc_links* link, ma_ug_t *ug);
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);
#define JUNK_COV 5
#define DISCARD_RATE 0.8