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for purge_dup

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chhylp123
2020-04-05 11:10:56 -04:00
parent 3c1d3cf6a1
commit ac3fcc339a
8 changed files with 4101 additions and 438 deletions
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Overlaps.h
+29 -5
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@@ -137,6 +137,16 @@ typedef struct {
ma_utg_t* F_seq;
} asg_t;
asg_t *asg_init(void);
void asg_destroy(asg_t *g);
void asg_arc_sort(asg_t *g);
void asg_seq_set(asg_t *g, int sid, int len, int del);
void asg_arc_index(asg_t *g);
void asg_cleanup(asg_t *g);
void asg_symm(asg_t *g);
void print_gfa(asg_t *g);
typedef struct { size_t n, m; uint64_t *a; } asg64_v;
@@ -373,6 +383,7 @@ typedef struct {
uint64_t i;
}kvec_asg_arc_t_warp;
void sort_kvec_t_u64_warp(kvec_t_u64_warp* u_vecs, uint32_t is_descend);
typedef struct {
@@ -777,7 +788,10 @@ R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
{
qn = node_min->a[b_min.readI]>>33;
if(reverse_sources[qn].length>=0) min_count++;
/************************BUG: don't forget****************************/
if(reverse_sources[qn].length > 0) min_count++;
///if(reverse_sources[qn].length >= 0) min_count++;
/************************BUG: don't forget****************************/
for (j = 0; j < (long long)reverse_sources[qn].length; j++)
{
tn = Get_tn(reverse_sources[qn].buffer[j]);
@@ -826,7 +840,10 @@ R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
{
qn = (b_min.b_0->b.a[b_min.untigI]>>1);
if(reverse_sources[qn].length>=0) min_count++;
/************************BUG: don't forget****************************/
if(reverse_sources[qn].length > 0) min_count++;
///if(reverse_sources[qn].length >= 0) min_count++;
/************************BUG: don't forget****************************/
for (j = 0; j < (long long)reverse_sources[qn].length; j++)
{
@@ -870,6 +887,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
}
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)
@@ -923,7 +941,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
{
qn = node_min->a[b_min.readI]>>33;
if(reverse_sources[qn].length>=0) min_count++;
if(reverse_sources[qn].length > 0) min_count++;
for (j = 0; j < (long long)reverse_sources[qn].length; j++)
{
tn = Get_tn(reverse_sources[qn].buffer[j]);
@@ -960,7 +978,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
{
qn = (b_min.b_0->b.a[b_min.untigI]>>1);
if(reverse_sources[qn].length>=0) min_count++;
if(reverse_sources[qn].length > 0) min_count++;
for (j = 0; j < (long long)reverse_sources[qn].length; j++)
{
@@ -1020,7 +1038,7 @@ void rescue_missing_overlaps_aggressive(ma_ug_t *i_ug, asg_t *r_g, ma_hit_t_allo
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);
void deduplicate(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);
long long maxShortUntig, float l_untig_rate, float max_node_threshold, R_to_U* ruIndex, uint32_t resolve_tangle);
void all_to_all_deduplicate(ma_ug_t* ug, uint8_t postive_flag, float drop_rate,
ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex);
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);
@@ -1032,5 +1050,11 @@ R_to_U* ruIndex, int max_hang, int min_ovlp, long long bubble_dist, uint32_t bac
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);
int unitig_arc_del_short_diploid_by_length(asg_t *g, float drop_ratio);
#define JUNK_COV 5
#define DISCARD_RATE 0.8
#endif