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keep k_trans

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chhylp123
2021-04-08 23:58:12 -04:00
parent 1a6f386823
commit 3218618bb4
4 changed files with 844 additions and 378 deletions
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Purge_Dups.h
+19
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@@ -24,6 +24,18 @@
#define XCY 2
#define YCX 3
#define Cal_Off(OFF) ((long long)((uint32_t)((OFF)>>32)) - (long long)((uint32_t)((OFF))))
#define Get_xOff(OFF) ((long long)((uint32_t)((OFF)>>32)))
#define Get_yOff(OFF) ((long long)((uint32_t)((OFF))))
#define Get_match(x) ((x).weight)
#define Get_total(x) ((x).index_beg)
#define Get_type(x) ((x).index_end)
#define Get_x_beg(x) ((x).x_beg_pos)
#define Get_x_end(x) ((x).x_end_pos)
#define Get_y_beg(x) ((x).y_beg_pos)
#define Get_y_end(x) ((x).y_end_pos)
#define Get_rev(x) ((x).rev)
typedef struct {
uint8_t rev;
uint8_t type;
@@ -66,5 +78,12 @@ void chain_trans_ovlp(hap_cov_t *cov, ma_ug_t *ug, asg_t *read_sg, buf_t* xReads
int get_specific_hap_overlap(kvec_hap_overlaps* x, uint32_t qn, uint32_t tn);
void set_reverse_hap_overlap(hap_overlaps* dest, hap_overlaps* source, uint32_t* types);
void print_hap_paf(ma_ug_t *ug, hap_overlaps* ovlp);
uint64_t get_xy_pos_by_pos(asg_t *read_g, asg_arc_t* t, uint32_t v_in_unitig, uint32_t w_in_unitig,
uint32_t v_in_pos, uint32_t w_in_pos, uint32_t xUnitigLen, uint32_t yUnitigLen, uint8_t* rev);
void quick_LIS(asg_arc_t_offset* x, uint32_t n, kvec_t_i32_warp* tailIndex, kvec_t_i32_warp* prevIndex);
uint32_t classify_hap_overlap(long long xBeg, long long xEnd, long long xLen,
long long yBeg, long long yEnd, long long yLen, long long* r_xBeg, long long* r_xEnd,
long long* r_yBeg, long long* r_yEnd);
int cmp_hap_alignment_chaining(const void * a, const void * b);
#endif