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chhylp123
2021-01-01 04:50:42 -05:00
parent c545fd84c7
commit 88f5b11f04
5 changed files with 747 additions and 3954 deletions
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Overlaps.cpp
+178 -3703
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File diff suppressed because it is too large Load Diff
Overlaps.h
+4 -23
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@@ -443,11 +443,8 @@ long long max_hang_length, long long clean_round, long long gap_fuzz,
float min_ovlp_drop_ratio, float max_ovlp_drop_ratio, char* output_file_name,
long long bubble_dist, int read_graph, int write);
void debug_info_of_specfic_read(char* name, ma_hit_t_alloc* sources,
ma_hit_t_alloc* reverse_sources, int id, char* command);
void debug_info_of_specfic_read(char* name, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, int id, char* command);
void collect_abnormal_edges(ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, long long readNum);
void add_overlaps(ma_hit_t_alloc* source_paf, ma_hit_t_alloc* dest_paf, uint64_t* source_index, long long listLen);
void remove_overlaps(ma_hit_t_alloc* source_paf, uint64_t* source_index, long long listLen);
void add_overlaps_from_different_sources(ma_hit_t_alloc* source_paf_list, ma_hit_t_alloc* dest_paf,
@@ -456,18 +453,6 @@ uint64_t* source_index, long long listLen);
#define EvaluateLen(U, id) ((U).a[(id)].start)
#define IsMerge(U, id) ((U).a[(id)].end)
#define kv_reuse(v, rn, rm, r) ((v).n = (rn), (v).m = (rm), (v).a = (r))
#define long_tip(U, id, threshold) ((EvaluateLen((U), (id))>=(threshold))&&(!((U).a[(id)].circ)))
///there are threee cases:
///1. if this untig is too long (>maxShortUntig), it must be not short untig/must be a long untig
///2. if this untig is long (>minLongUntig && EvaluateLen(ug->u, av[i].v>>1) > (EvaluateLen(ug->u, v>>1)*l_untig_rate)), it might be a long tip
#define check_long_tip(U, id, minLongUntig, maxShortUntig, ShortUntigRate, mainLen) \
((!((U).a[(id)].circ)) \
&& \
((EvaluateLen((U), (id)) > (maxShortUntig))\
||\
((long_tip((U), (id), (minLongUntig)))\
&&\
(EvaluateLen((U), (id)) > (ShortUntigRate)*(mainLen)))))
#define Get_vis(visit, v, d) (((visit)[(v)>>1])&(((((v)<<(d))&1)+1)))
#define Set_vis(visit, v, d) (((visit)[(v)>>1])|=(((((v)<<(d))&1)+1)))
@@ -486,10 +471,6 @@ void set_R_to_U(R_to_U* x, uint32_t rID, uint32_t uID, uint32_t is_Unitig);
void get_R_to_U(R_to_U* x, uint32_t rID, uint32_t* uID, uint32_t* is_Unitig);
void transfor_R_to_U(R_to_U* x);
void debug_utg_graph(ma_ug_t *ug, asg_t* read_g, int require_equal_nv, int test_tangle);
void clean_untig_graph(ma_ug_t *ug, asg_t *read_g, ma_hit_t_alloc* reverse_sources,
long long bubble_dist, long long tipsLen, float tip_drop_ratio, long long stops_threshold,
R_to_U* ruIndex, buf_t* b_0, uint8_t* visit, float density, uint32_t miniHapLen,
uint32_t miniBiGraph, float chimeric_rate, int is_final_clean);
int asg_pop_bubble_primary(asg_t *g, int max_dist);
long long asg_arc_del_simple_circle_untig(ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, asg_t *g, long long circleLen, int is_drop);
@@ -1041,8 +1022,6 @@ uint32_t is_primary_check, kvec_asg_arc_t_warp* new_rtg_edges, kvec_t_u32_warp*
void rescue_missing_overlaps_aggressive(ma_ug_t *i_ug, asg_t *r_g, ma_hit_t_alloc* sources, ma_sub_t *coverage_cut,
R_to_U* ruIndex, int max_hang, int min_ovlp, long long bubble_dist, uint32_t is_bubble_check,
uint32_t is_primary_check, kvec_asg_arc_t_warp* new_rtg_edges);
void deduplicate(ma_ug_t *src, asg_t *read_g, ma_hit_t_alloc* reverse_sources, long long minLongUntig,
long long maxShortUntig, float l_untig_rate, float max_node_threshold, R_to_U* ruIndex, uint32_t resolve_tangle);
void all_to_all_deduplicate(ma_ug_t* ug, asg_t* read_g, ma_sub_t* coverage_cut,
ma_hit_t_alloc* sources, uint8_t postive_flag, float drop_rate, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, float double_check_rate);
void drop_semi_circle(ma_ug_t *ug, asg_t* nsg, asg_t* read_g, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex);
@@ -1055,7 +1034,7 @@ uint32_t is_bubble_check, uint32_t is_primary_check);
uint32_t get_edge_from_source(ma_hit_t_alloc* sources, ma_sub_t *coverage_cut,
R_to_U* ruIndex, int max_hang, int min_ovlp, uint32_t query, uint32_t target, asg_arc_t* t);
uint64_t asg_bub_pop1_primary_trio(asg_t *g, ma_ug_t *utg, uint32_t v0, int max_dist, buf_t *b,
uint32_t positive_flag, uint32_t negative_flag, uint32_t is_pop, uint64_t* path_base_len);
uint32_t positive_flag, uint32_t negative_flag, uint32_t is_pop, uint64_t* path_base_len, uint64_t* path_nodes);
int unitig_arc_del_short_diploid_by_length(asg_t *g, float drop_ratio);
@@ -1102,6 +1081,8 @@ uint8_t flag, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, long lon
long long tipsLen, float tip_drop_ratio, long long stops_threshold, R_to_U* ruIndex,
float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench);
asg_t* copy_read_graph(asg_t *src);
ma_ug_t *ma_ug_gen(asg_t *g);
void ma_ug_destroy(ma_ug_t *ug);
#define JUNK_COV 5
#define DISCARD_RATE 0.8
Purge_Dups.cpp
+1 -1
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@@ -3292,7 +3292,7 @@ int asg_pop_bubble_purge_graph(asg_t *purge_g, int max_dist)
for (i = 0; i < nv; ++i) // asg_bub_pop1() may delete some edges/arcs
if (!av[i].del) ++n_arc;
if (n_arc > 1)
n_pop += asg_bub_pop1_primary_trio(purge_g, NULL, v, max_dist, &b, (uint32_t)-1, DROP, 1, NULL);
n_pop += asg_bub_pop1_primary_trio(purge_g, NULL, v, max_dist, &b, (uint32_t)-1, DROP, 1, NULL, NULL);
}
free(b.a); free(b.S.a); free(b.T.a); free(b.b.a); free(b.e.a);
if (n_pop) asg_cleanup(purge_g);
hic.cpp
+543 -227
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File diff suppressed because it is too large Load Diff
hic.h
+21
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@@ -14,4 +14,25 @@ void push_hc_edge(hc_linkeage* x, uint64_t uID, int weight, int dir, uint64_t* d
void hic_analysis(ma_ug_t *ug, asg_t* read_g, hc_links* link);
void hic_benchmark(ma_ug_t *ug, asg_t* read_g);
typedef struct {
uint32_t* index;
ma_ug_t* ug;
kvec_t(uint32_t) list;
kvec_t(uint32_t) num;
kvec_t(uint64_t) pathLen;
kvec_t(uint64_t) b_s_idx;
uint64_t f_bub, b_bub;
asg_t *b_g;
} bubble_type;
#define P_het(B) ((B).num.n)
#define M_het(B) ((B).num.n + 1)
// #define IF_BUB(ID, B) ((B).index[(ID)] < (B).num.n)
// #define IF_HET(ID, B) ((B).index[(ID)] == (B).num.n)
// #define IF_HOM(ID, B) ((B).index[(ID)] > (B).num.n)
#define IF_BUB(ID, B) ((B).index[(ID)] < (B).f_bub+1)
#define IF_HET(ID, B) ((B).index[(ID)] == (B).f_bub+1)
#define IF_HOM(ID, B) ((B).index[(ID)] > (B).f_bub+1)
#define Get_bub_num(RECORD) ((RECORD).num.n-1)
void get_bubbles(bubble_type* bub, uint64_t id, uint32_t* beg, uint32_t* sink, uint32_t** a, uint32_t* n, uint64_t* pathBase);
#endif