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new somatic variant popping

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chhylp123
2021-05-19 09:52:40 -04:00
parent be8e1e3117
commit b12e008416
5 changed files with 562 additions and 84 deletions
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Overlaps.h
+15
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@@ -1228,6 +1228,21 @@ void ma_ug_print(const ma_ug_t *ug, asg_t* read_g, const ma_sub_t *coverage_cut,
ma_hit_t_alloc* sources, R_to_U* ruIndex, const char* prefix, FILE *fp);
void ma_ug_print_simple(const ma_ug_t *ug, asg_t* read_g, const ma_sub_t *coverage_cut,
ma_hit_t_alloc* sources, R_to_U* ruIndex, const char* prefix, FILE *fp);
trans_chain* init_trans_chain(ma_ug_t *ug, uint64_t r_num);
void destory_trans_chain(trans_chain **x);
typedef struct {///[cBeg, cEnd)
uint32_t u_i, r_i, len, s_pos_cur, s_pre_v, s_pre_w, p_v, p_idx, p_uId, cBeg, cEnd;
///buf_t* x;
uint32_t *a, an;
ma_ug_t *ug;
asg_t *read_sg;
trans_chain* t_ch;
} u_trans_hit_idx;
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);
#define JUNK_COV 5
#define DISCARD_RATE 0.8