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haplotype popping

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chhylp123
2021-05-24 19:43:50 -04:00
parent 9e6dde7fb2
commit a39f01f4d8
9 changed files with 1696 additions and 567 deletions
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Overlaps.h
+41 -3
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@@ -120,6 +120,7 @@ typedef struct {
uint32_t occ;
double nw;
uint8_t f:6, rev:1, del:1;
uint8_t qo:4, to:4;
} u_trans_t;
typedef struct {
@@ -401,7 +402,6 @@ typedef struct {
kvec_t(uint32_t) e; // visited edges/arcs
} buf_t;
typedef struct {
kvec_t(uint64_t) Nodes;
kvec_t(uint64_t) Edges;
@@ -858,13 +858,44 @@ typedef struct{
hc_edge *a;
}hc_edge_warp;
typedef struct {
uint32_t qs, qe, qn, qus, que;
uint32_t ts, te, tn, tus, tue;
} utg_thit_t;
typedef struct {
size_t n, m;
utg_thit_t* a;
} kv_utg_thit_t_t;
typedef struct {
ma_hit_t_alloc* reverse_sources;
ma_sub_t *coverage_cut;
R_to_U* ruIndex;
asg_t *read_g;
kvec_asg_arc_t_offset u_buffer;
kvec_t_i32_warp tailIndex;
kvec_t_i32_warp prevIndex;
kv_utg_thit_t_t k_t_b;
kv_ca_buf_t c_buf;
kv_u_trans_t k_trans;
uint64_t *pos_idx, rn;
kvec_t(uint32_t) topo_res;
ma_ug_t *cug;
int max_hang;
int min_ovlp;
ma_utg_v u;
kv_u_trans_t t;
buf_t b0, b1;
} utg_trans_t;
void init_hc_links(hc_links* link, uint64_t ug_num, trans_chain* t_ch);
void destory_hc_links(hc_links* link);
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, uint32_t is_update_chain);
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, uint32_t is_update_chain, uint32_t keep_d);
uint32_t negative_flag, uint32_t is_pop, uint64_t* path_base_len, uint64_t* path_nodes, hap_cov_t *cov, uint32_t is_update_chain, uint32_t keep_d, utg_trans_t *o);
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,
@@ -951,6 +982,13 @@ typedef struct {///[cBeg, cEnd)
void reset_u_trans_hit_idx(u_trans_hit_idx *t, uint32_t* i_x_a, uint32_t i_x_n, ma_ug_t *i_ug,
asg_t *i_read_sg, trans_chain* i_t_ch, uint32_t i_cBeg, uint32_t i_cEnd);
uint32_t get_u_trans_hit(u_trans_hit_idx *t, u_trans_hit_t *hit);
inline uint32_t get_offset_adjust(uint32_t offset, uint32_t offsetLen, uint32_t targetLen)
{
return ((double)(offset)/(double)(offsetLen))*targetLen;
}
uint32_t set_utg_offset(uint32_t *a, uint32_t a_n, ma_ug_t *ug, asg_t *read_sg, uint64_t* pos_idx, uint32_t is_clear,
uint32_t only_len);
#define JUNK_COV 5
#define DISCARD_RATE 0.8