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prepare for further changes

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This commit is contained in:
Heng Li
2020-06-06 21:55:41 -04:00
parent 97f6efc4da
commit afa93e4bbb
14 changed files with 459 additions and 465 deletions
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Overlaps.h
+21 -3
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@@ -83,6 +83,7 @@ char* output_file_name);
typedef struct {
uint32_t s:31, del:1, e;
uint8_t c;
uint8_t weak_contain;
} ma_sub_t;
void ma_hit_sub(int min_dp, ma_hit_t_alloc* sources, long long n_read, uint64_t* readLen,
@@ -103,7 +104,6 @@ typedef struct {
uint8_t no_l_indel;
} asg_arc_t;
typedef struct {
uint32_t len:31, circ:1; // len: length of the unitig; circ: circular if non-zero
uint32_t start, end; // start: starting vertex in the string graph; end: ending vertex
@@ -112,11 +112,10 @@ typedef struct {
char *s; // unitig sequence is not null
} ma_utg_t;
typedef struct {
uint32_t len:31, del:1;
uint8_t c;
uint8_t weak_contain;
} asg_seq_t;
typedef struct {
@@ -128,6 +127,10 @@ typedef struct {
asg_seq_t *seq;
uint64_t *idx;
uint32_t m_con, n_con;
uint64_t *contain;
uint64_t *con_idx;
uint8_t* seq_vis;
uint32_t n_F_seq;
@@ -505,6 +508,21 @@ void init_Edge_iter(asg_t* g, uint32_t v, asg_arc_t* new_edges, uint32_t new_edg
int get_arc_t(Edge_iter* x, asg_arc_t* get);
int asg_pop_bubble_primary_trio(ma_ug_t *ug, int max_dist, uint32_t positive_flag, uint32_t negative_flag);
/*************************************
* Routines modified for containment *
*************************************/
void delete_single_edge(ma_hit_t_alloc *sources, const ma_sub_t *coverage_cut, uint32_t qn, uint32_t tn);
void delete_all_edges(ma_hit_t_alloc *sources, ma_sub_t *coverage_cut, uint32_t qn);
void ma_hit_contained_advance(ma_hit_t_alloc *sources, long long n_read, ma_sub_t *coverage_cut, R_to_U *ruIndex, int max_hang, int min_ovlp);
void asg_con_sort(asg_t *g);
void asg_con_index(asg_t *g);
asg_t *ma_sg_gen(const ma_hit_t_alloc* sources, long long n_read, const ma_sub_t *coverage_cut, int max_hang, int min_ovlp);
int asg_arc_del_trans(asg_t *g, int fuzz);
/*******************
* Other rountines *
*******************/
inline int get_real_length(asg_t *g, uint32_t v, uint32_t* v_s)
{