mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-10 14:20:56 +08:00
r852 -> hybrid correction
This commit is contained in:
chhylp123
+95
-95
@@ -1,96 +1,96 @@
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#ifndef __PURGEDUPS__
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#define __PURGEDUPS__
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#define __STDC_LIMIT_MACROS
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#include <stdio.h>
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#include <stdint.h>
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#include "kvec.h"
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#include "kdq.h"
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#include "Overlaps.h"
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#include "Hash_Table.h"
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#define COV_COUNT 1024
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#define HOM_PEAK_RATE 1.25
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#define HET_PEAK_RATE (HOM_PEAK_RATE*2)
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#define ALTER_COV_THRES 0.9
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#define REAL_ALTER_THRES 0.25
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#define CHAIN_FILTER_RATE 0.7
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#define REV_W 8
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#define SELF_EXIST 0
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#define REVE_EXIST 1
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#define DELETE 2
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#define MIXED 3
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#define FLIP 4
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#define X2Y 0
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#define Y2X 1
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#define XCY 2
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#define YCX 3
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#define Cal_Off(OFF) ((long long)((uint32_t)((OFF)>>32)) - (long long)((uint32_t)((OFF))))
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#define Get_xOff(OFF) ((long long)((uint32_t)((OFF)>>32)))
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#define Get_yOff(OFF) ((long long)((uint32_t)((OFF))))
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#define Get_match(x) ((x).weight)
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#define Get_total(x) ((x).index_beg)
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#define Get_type(x) ((x).index_end)
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#define Get_x_beg(x) ((x).x_beg_pos)
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#define Get_x_end(x) ((x).x_end_pos)
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#define Get_y_beg(x) ((x).y_beg_pos)
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#define Get_y_end(x) ((x).y_end_pos)
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#define Get_rev(x) ((x).rev)
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typedef struct {
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uint8_t rev;
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uint8_t type;
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uint8_t status;
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uint32_t x_beg_pos;
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uint32_t x_end_pos;
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uint32_t y_beg_pos;
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uint32_t y_end_pos;
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uint32_t x_beg_id;
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uint32_t x_end_id;
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uint32_t y_beg_id;
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uint32_t y_end_id;
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uint32_t xUid;
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uint32_t yUid;
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uint32_t weight;
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long long score;
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float s;
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}hap_overlaps;
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typedef struct {
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kvec_t(hap_overlaps) a;
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}kvec_hap_overlaps;
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typedef struct {
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kvec_hap_overlaps* x;
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uint32_t num;
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}hap_overlaps_list;
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void purge_dups(ma_ug_t *ug, asg_t *read_g, ma_sub_t* coverage_cut, ma_hit_t_alloc* sources,
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ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, kvec_asg_arc_t_warp* edge, float density,
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uint32_t purege_minLen, int max_hang, int min_ovlp, float drop_ratio, uint32_t just_contain,
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uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans, uint32_t collect_p_trans_f);
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void fill_unitig(uint64_t* buffer, uint32_t bufferLen, asg_t* read_g, kvec_asg_arc_t_warp* edge,
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uint32_t is_circle, uint64_t* rLen);
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void get_contig_length(ma_ug_t *ug, asg_t *g, uint64_t* primaryLen, uint64_t* alterLen);
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void enable_debug_mode(uint32_t mode);
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hap_cov_t* init_hap_cov_t(ma_ug_t *ug, asg_t* read_g, ma_hit_t_alloc* sources, R_to_U* ruIndex, ma_hit_t_alloc* reverse_sources,
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ma_sub_t *coverage_cut, int max_hang, int min_ovlp, uint32_t is_collect_trans);
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void destory_hap_cov_t(hap_cov_t **x);
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void chain_trans_ovlp(hap_cov_t *cov, utg_trans_t *o, ma_ug_t *ug, asg_t *read_sg, buf_t* xReads, uint32_t targetBaseLen, uint32_t* xEnd);
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int get_specific_hap_overlap(kvec_hap_overlaps* x, uint32_t qn, uint32_t tn);
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void set_reverse_hap_overlap(hap_overlaps* dest, hap_overlaps* source, uint32_t* types);
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void print_hap_paf(ma_ug_t *ug, hap_overlaps* ovlp);
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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,
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uint32_t v_in_pos, uint32_t w_in_pos, uint32_t xUnitigLen, uint32_t yUnitigLen, uint8_t* rev);
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void quick_LIS(asg_arc_t_offset* x, uint32_t n, kvec_t_i32_warp* tailIndex, kvec_t_i32_warp* prevIndex);
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uint32_t classify_hap_overlap(long long xBeg, long long xEnd, long long xLen,
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long long yBeg, long long yEnd, long long yLen, long long* r_xBeg, long long* r_xEnd,
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long long* r_yBeg, long long* r_yEnd);
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int cmp_hap_alignment_chaining(const void * a, const void * b);
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uint32_t classify_hap_overlap(long long xBeg, long long xEnd, long long xLen,
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long long yBeg, long long yEnd, long long yLen, long long* r_xBeg, long long* r_xEnd,
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long long* r_yBeg, long long* r_yEnd);
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#ifndef __PURGEDUPS__
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#define __PURGEDUPS__
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#define __STDC_LIMIT_MACROS
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#include <stdio.h>
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#include <stdint.h>
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#include "kvec.h"
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#include "kdq.h"
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#include "Overlaps.h"
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#include "Hash_Table.h"
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#define COV_COUNT 1024
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#define HOM_PEAK_RATE 1.25
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#define HET_PEAK_RATE (HOM_PEAK_RATE*2)
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#define ALTER_COV_THRES 0.9
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#define REAL_ALTER_THRES 0.25
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#define CHAIN_FILTER_RATE 0.7
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#define REV_W 8
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#define SELF_EXIST 0
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#define REVE_EXIST 1
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#define DELETE 2
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#define MIXED 3
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#define FLIP 4
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#define X2Y 0
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#define Y2X 1
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#define XCY 2
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#define YCX 3
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#define Cal_Off(OFF) ((long long)((uint32_t)((OFF)>>32)) - (long long)((uint32_t)((OFF))))
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#define Get_xOff(OFF) ((long long)((uint32_t)((OFF)>>32)))
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#define Get_yOff(OFF) ((long long)((uint32_t)((OFF))))
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#define Get_match(x) ((x).weight)
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#define Get_total(x) ((x).index_beg)
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#define Get_type(x) ((x).index_end)
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#define Get_x_beg(x) ((x).x_beg_pos)
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#define Get_x_end(x) ((x).x_end_pos)
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#define Get_y_beg(x) ((x).y_beg_pos)
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#define Get_y_end(x) ((x).y_end_pos)
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#define Get_rev(x) ((x).rev)
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typedef struct {
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uint8_t rev;
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uint8_t type;
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uint8_t status;
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uint32_t x_beg_pos;
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uint32_t x_end_pos;
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uint32_t y_beg_pos;
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uint32_t y_end_pos;
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uint32_t x_beg_id;
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uint32_t x_end_id;
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uint32_t y_beg_id;
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uint32_t y_end_id;
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uint32_t xUid;
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uint32_t yUid;
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uint32_t weight;
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long long score;
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float s;
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}hap_overlaps;
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typedef struct {
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kvec_t(hap_overlaps) a;
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}kvec_hap_overlaps;
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typedef struct {
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kvec_hap_overlaps* x;
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uint32_t num;
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}hap_overlaps_list;
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void purge_dups(ma_ug_t *ug, asg_t *read_g, ma_sub_t* coverage_cut, ma_hit_t_alloc* sources,
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ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, kvec_asg_arc_t_warp* edge, float density,
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uint32_t purege_minLen, int max_hang, int min_ovlp, float drop_ratio, uint32_t just_contain,
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uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans, uint32_t collect_p_trans_f);
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void fill_unitig(uint64_t* buffer, uint32_t bufferLen, asg_t* read_g, kvec_asg_arc_t_warp* edge,
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uint32_t is_circle, uint64_t* rLen);
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void get_contig_length(ma_ug_t *ug, asg_t *g, uint64_t* primaryLen, uint64_t* alterLen);
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void enable_debug_mode(uint32_t mode);
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hap_cov_t* init_hap_cov_t(ma_ug_t *ug, asg_t* read_g, ma_hit_t_alloc* sources, R_to_U* ruIndex, ma_hit_t_alloc* reverse_sources,
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ma_sub_t *coverage_cut, int max_hang, int min_ovlp, uint32_t is_collect_trans);
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void destory_hap_cov_t(hap_cov_t **x);
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void chain_trans_ovlp(hap_cov_t *cov, utg_trans_t *o, ma_ug_t *ug, asg_t *read_sg, buf_t* xReads, uint32_t targetBaseLen, uint32_t* xEnd);
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int get_specific_hap_overlap(kvec_hap_overlaps* x, uint32_t qn, uint32_t tn);
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void set_reverse_hap_overlap(hap_overlaps* dest, hap_overlaps* source, uint32_t* types);
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void print_hap_paf(ma_ug_t *ug, hap_overlaps* ovlp);
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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,
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uint32_t v_in_pos, uint32_t w_in_pos, uint32_t xUnitigLen, uint32_t yUnitigLen, uint8_t* rev);
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void quick_LIS(asg_arc_t_offset* x, uint32_t n, kvec_t_i32_warp* tailIndex, kvec_t_i32_warp* prevIndex);
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uint32_t classify_hap_overlap(long long xBeg, long long xEnd, long long xLen,
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long long yBeg, long long yEnd, long long yLen, long long* r_xBeg, long long* r_xEnd,
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long long* r_yBeg, long long* r_yEnd);
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int cmp_hap_alignment_chaining(const void * a, const void * b);
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uint32_t classify_hap_overlap(long long xBeg, long long xEnd, long long xLen,
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long long yBeg, long long yEnd, long long yLen, long long* r_xBeg, long long* r_xEnd,
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long long* r_yBeg, long long* r_yEnd);
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#endif
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