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for high-het and coverage

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chhylp123
2020-07-28 13:07:35 -04:00
parent 94008c02ac
commit ace34ae2b8
12 changed files with 1902 additions and 89 deletions
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Correct.h
+11 -4
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@@ -1162,10 +1162,17 @@ void init_Cigar_record_alloc(Cigar_record_alloc* x);
void resize_Cigar_record_alloc(Cigar_record_alloc* x, long long new_size);
void destory_Cigar_record_alloc(Cigar_record_alloc* x);
void afine_gap_alignment(const char *tseq, uint8_t* tnum, const int tl,
const char *qseq, uint8_t* qnum, const int ql, const uint8_t *c2n, const int strand,
void afine_gap_alignment(const char *qseq, uint8_t* qnum, const int ql,
const char *tseq, uint8_t* tnum, const int tl, const uint8_t *c2n, const int strand,
int sc_mch, int sc_mis, int gapo, int gape, int bandLen, int zdrop, int end_bonus,
long long* max_t_pos, long long* max_q_pos, long long* score, long long* droped);
long long* max_q_pos, long long* max_t_pos, long long* global_score,
long long* extention_score, long long* q_boundary_score, long long* q_boundary_t_coordinate,
long long* t_boundary_score, long long* t_boundary_q_coordinate,
long long* droped, int mode);
void correct_overlap_high_het(overlap_region_alloc* overlap_list, All_reads* R_INF,
UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read);
long long get_affine_gap_score(overlap_region* ovc, UC_Read* g_read, UC_Read* overlap_read, uint8_t* x_num,
uint8_t* y_num, uint64_t EstimateXOlen, uint64_t EstimateYOlen);
#define FORWARD_KSW 0
#define BACKWARD_KSW 1
@@ -1174,5 +1181,5 @@ long long* max_t_pos, long long* max_q_pos, long long* score, long long* droped)
#define GAP_OPEN_KSW 4
#define GAP_EXT_KSW 2
#define Z_DROP_KSW 400
#define BAND_KSW 50
#define BAND_KSW 500
#endif