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https://github.com/chhylp123/hifiasm.git
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final DP-based assembly
This commit is contained in:
Haoyu Cheng
+322
@@ -0,0 +1,322 @@
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#ifndef __OVERLAPS__
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#define __OVERLAPS__
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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 "Hash_Table.h"
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///#define MIN_OVERLAP_LEN 2000
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///#define MIN_OVERLAP_LEN 500
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#define MIN_OVERLAP_LEN 50
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#define MIN_OVERLAP_COVERAGE 1
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#define MAX_HANG_LEN 1000
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#define MAX_HANG_PRE 0.8
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#define GAP_FUZZ 1000
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#define MAX_SHORT_TIPS 3
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#define MAX_BUBBLE_DIST 10000000
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#define SMALL_BUBBLE_SIZE (uint32_t)-1
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//#define SMALL_BUBBLE_SIZE 1000
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#define Get_qn(RECORD) ((uint32_t)((RECORD).qns>>32))
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#define Get_qs(RECORD) ((uint32_t)((RECORD).qns))
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#define Get_qe(RECORD) ((RECORD).qe)
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#define Get_tn(RECORD) ((RECORD).tn)
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#define Get_ts(RECORD) ((RECORD).ts)
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#define Get_te(RECORD) ((RECORD).te)
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#define LONG_TIPS 0
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#define TWO_INPUT 1
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#define TWO_OUTPUT 2
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#define MUL_INPUT 3
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#define MUL_OUTPUT 4
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#define END_TIPS 5
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#define LONG_TIPS_UNDER_MAX_EXT 6
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#define LOOP 7
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///query is the read itself
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typedef struct {
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uint64_t qns;
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uint32_t qe, tn, ts, te;
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uint32_t ml:31, rev:1;
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uint32_t bl:31, del:1;
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uint8_t el;
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} ma_hit_t;
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typedef struct {
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ma_hit_t* buffer;
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uint32_t size;
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uint32_t length;
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uint8_t is_fully_corrected;
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} ma_hit_t_alloc;
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void init_ma_hit_t_alloc(ma_hit_t_alloc* x);
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void clear_ma_hit_t_alloc(ma_hit_t_alloc* x);
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void resize_ma_hit_t_alloc(ma_hit_t_alloc* x, uint64_t size);
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void destory_ma_hit_t_alloc(ma_hit_t_alloc* x);
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void add_ma_hit_t_alloc(ma_hit_t_alloc* x, ma_hit_t* element);
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void ma_hit_sort_tn(ma_hit_t *a, long long n);
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void ma_hit_sort_qns(ma_hit_t *a, long long n);
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int load_all_data_from_disk(ma_hit_t_alloc **sources, ma_hit_t_alloc **reverse_sources,
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char* output_file_name);
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typedef struct {
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ma_hit_t_alloc overlaps;
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} Assembly_Graph;
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void init_Assembly_Graph(Assembly_Graph* x);
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void destory_Assembly_Graph(Assembly_Graph* x);
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void collect_ma_hit_t(ma_hit_t_alloc* dest, ma_hit_t_alloc* sources, long long num_sources);
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void normalize_ma_hit_t(ma_hit_t_alloc* sources, long long num_sources);
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void debug_normalize_ma_hit_t(ma_hit_t_alloc* sources, long long num_sources);
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typedef struct {
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uint32_t s:31, del:1, e;
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} ma_sub_t;
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void ma_hit_sub(int min_dp, ma_hit_t_alloc* sources, long long n_read, uint64_t* readLen,
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long long mini_overlap_length, ma_sub_t** coverage_cut);
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void ma_hit_cut(int min_dp, ma_hit_t_alloc* sources, long long n_read, uint64_t* readLen,
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long long mini_overlap_length, ma_sub_t** coverage_cut);
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void ma_hit_flt(ma_hit_t_alloc* sources, long long n_read, const ma_sub_t *coverage_cut,
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int max_hang, int min_ovlp);
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long long get_specific_overlap(ma_hit_t_alloc* x, uint32_t qn, uint32_t tn);
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void debug_cut_ma_hit_t(ma_hit_t_alloc* sources, long long num_sources, ma_sub_t *coverage_cut);
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typedef struct {
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uint64_t ul;
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uint32_t v;
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uint32_t ol:31, del:1;
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uint8_t strong;
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uint8_t el;
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} asg_arc_t;
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typedef struct {
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uint32_t len:31, del:1;
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} asg_seq_t;
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typedef struct {
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uint32_t m_arc, n_arc:31, is_srt:1;
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asg_arc_t *arc;
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uint32_t m_seq, n_seq:31, is_symm:1;
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asg_seq_t *seq;
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uint64_t *idx;
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uint8_t* seq_vis;
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} asg_t;
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typedef struct { size_t n, m; uint64_t *a; } asg64_v;
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#define MA_HT_INT (-1)
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#define MA_HT_QCONT (-2)
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#define MA_HT_TCONT (-3)
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#define MA_HT_SHORT_OVLP (-4)
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///in default, max_hang = 1000, int_frac = 0.05, min_ovlp = 2000
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static inline int ma_hit2arc(const ma_hit_t *h, int ql, int tl, int max_hang, float int_frac, int min_ovlp, asg_arc_t *p)
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{
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int32_t tl5, tl3, ext5, ext3, qs = (int32_t)h->qns;
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uint32_t u, v, l; // u: query end; v: target end; l: length from u to v
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///if query and target are in different strand
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if (h->rev) tl5 = tl - h->te, tl3 = h->ts; // tl5: 5'-end overhang (on the query strand); tl3: similar
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else tl5 = h->ts, tl3 = tl - h->te;
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///ext5 and ext3 is the hang on left side and right side, respectively
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ext5 = qs < tl5? qs : tl5;
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ext3 = ql - h->qe < tl3? ql - h->qe : tl3;
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/**
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if (ext5 > max_hang || ext3 > max_hang || h->qe - qs < (h->qe - qs + ext5 + ext3) * int_frac)
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return MA_HT_INT;
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**/
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if (ext5 > max_hang || ext3 > max_hang
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|| h->qe - qs < (h->qe - qs + ext5 + ext3) * int_frac
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|| h->te - h->ts < (h->te - h->ts + ext5 + ext3) * int_frac)
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{
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return MA_HT_INT;
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}
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/**
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********************************query-to-target overlap****************************
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case 1: u = 0, rev = 0 in the view of target: direction is 1
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query: CCCCCCCCTAATTAAAAT target: TAATTAAAATGGGGGG (use ex-target as query)
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|||||||||| <---> ||||||||||
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target: TAATTAAAATGGGGGG query: CCCCCCCCTAATTAAAAT (use ex-query as target)
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case 2: u = 0, rev = 1 in the view of target: direction is 0
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query: CCCCCCCCTAATTAAAAT target: CCCCCCATTTTAATTA (use ex-target as query)
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|||||||||| <---> ||||||||||
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target: TAATTAAAATGGGGGG query: ATTTTAATTAGGGGGGGG (use ex-query as target)
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********************************query-to-target overlap****************************
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********************************target-to-query overlap****************************
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case 3: u = 1, rev = 0 in the view of target: direction is 0
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query: AAATAATATCCCCCCGCG target: GGGCCGGCAAATAATAT (use ex-target as query)
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||||||||| <---> |||||||||
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target: GGGCCGGCAAATAATAT query: AAATAATATCCCCCCGCG (use ex-query as target)
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case 4: u = 1, rev = 1 in the view of target: direction is 1
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query: AAATAATATCCCCCCGCG target: ATATTATTTGCCGGCCC (use ex-target as query)
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||||||||| <---> |||||||||
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target: GGGCCGGCAAATAATAT query: CGCGGGGGATATTATTT (use ex-query as target)
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********************************target-to-query overlap****************************
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**/
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if (qs <= tl5 && ql - h->qe <= tl3) return MA_HT_QCONT; // query contained in target
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else if (qs >= tl5 && ql - h->qe >= tl3) return MA_HT_TCONT; // target contained in query
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else if (qs > tl5) u = 0, v = !!h->rev, l = qs - tl5; ///u = 0 means query-to-target overlap, l is the length of node in string graph (not the overlap length)
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else u = 1, v = !h->rev, l = (ql - h->qe) - tl3; ///u = 1 means target-to-query overlaps, l is the length of node in string graph (not the overlap length)
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if (h->qe - qs + ext5 + ext3 < min_ovlp || h->te - h->ts + ext5 + ext3 < min_ovlp) return MA_HT_SHORT_OVLP; // short overlap
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///u = 0 / 1 means query-to-target / target-to-query overlaps,
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///l is the length of node in string graph (not the overlap length between two reads)
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u |= h->qns>>32<<1, v |= h->tn<<1;
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/**
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p->ul: |____________31__________|__________1___________|______________32_____________|
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qn direction of overlap length of this node (not overlap length)
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(in the view of query)
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p->v : |___________31___________|__________1___________|
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tn reverse direction of overlap
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(in the view of target)
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p->ol: overlap length
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**/
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p->ul = (uint64_t)u<<32 | l, p->v = v, p->ol = ql - l, p->del = 0;
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///l is the length of node in string graph (not the overlap length)
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p->strong = h->ml;
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p->el = h->el;
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return l;
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}
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void build_string_graph(int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, long long n_read, uint64_t* readLen,
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long long mini_overlap_length, long long max_hang_length,
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long long clean_round, float min_ovlp_drop_ratio, float max_ovlp_drop_ratio,
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float final_ovlp_drop_ratio, char* output_file_name, long long bubble_dist);
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#define asg_arc_len(arc) ((uint32_t)(arc).ul)
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#define asg_arc_n(g, v) ((uint32_t)(g)->idx[(v)])
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#define asg_arc_a(g, v) (&(g)->arc[(g)->idx[(v)]>>32])
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// append an arc
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static inline asg_arc_t *asg_arc_pushp(asg_t *g)
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{
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if (g->n_arc == g->m_arc) {
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g->m_arc = g->m_arc? g->m_arc<<1 : 16;
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g->arc = (asg_arc_t*)realloc(g->arc, g->m_arc * sizeof(asg_arc_t));
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}
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return &g->arc[g->n_arc++];
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}
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// set asg_arc_t::del for v->w
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static inline void asg_arc_del(asg_t *g, uint32_t v, uint32_t w, int del)
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{
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uint32_t i, nv = asg_arc_n(g, v);
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asg_arc_t *av = asg_arc_a(g, v);
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for (i = 0; i < nv; ++i)
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if (av[i].v == w) av[i].del = !!del;
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}
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// set asg_arc_t::del and asg_seq_t::del to 1 for sequence s and all its associated arcs
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static inline void asg_seq_del(asg_t *g, uint32_t s)
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{
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uint32_t k;
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g->seq[s].del = 1;
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for (k = 0; k < 2; ++k) {
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uint32_t i, v = s<<1 | k;
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uint32_t nv = asg_arc_n(g, v);
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asg_arc_t *av = asg_arc_a(g, v);
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for (i = 0; i < nv; ++i) {
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av[i].del = 1;
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asg_arc_del(g, av[i].v^1, v^1, 1);
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}
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}
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}
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typedef struct {
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uint32_t len:31, circ:1; // len: length of the unitig; circ: circular if non-zero
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uint32_t start, end; // start: starting vertex in the string graph; end: ending vertex
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uint32_t m, n; // number of reads
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uint64_t *a; // list of reads
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char *s; // unitig sequence is not null
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} ma_utg_t;
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typedef struct { size_t n, m; ma_utg_t *a; } ma_utg_v;
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typedef struct {
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ma_utg_v u;
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asg_t *g;
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} ma_ug_t;
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typedef struct {
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uint32_t utg:31, ori:1, start, len;
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} utg_intv_t;
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/******************
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* Bubble popping *
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******************/
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typedef struct {
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uint32_t p; // the optimal parent vertex
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uint32_t d; // the shortest distance from the initial vertex
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uint32_t c; // max count of reads
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uint32_t r:31, s:1; // r: the number of remaining incoming arc; s: state
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//s: state, s=0, this edge has not been visited, otherwise, s=1
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} binfo_t;
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typedef struct {
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///all information for each node
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binfo_t *a;
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kvec_t(uint32_t) S; // set of vertices without parents, nodes with all incoming edges visited
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kvec_t(uint32_t) T; // set of tips
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kvec_t(uint32_t) b; // visited vertices
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kvec_t(uint32_t) e; // visited edges/arcs
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} buf_t;
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// count the number of outgoing arcs, including reduced arcs
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static inline int count_out_with_del(const asg_t *g, uint32_t v)
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{
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uint32_t i, n, nv = asg_arc_n(g, v);
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const asg_arc_t *av = asg_arc_a(g, v);
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/**
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for (i = n = 0; i < nv; ++i)
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if (!av[i].del) ++n;
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return n;
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**/
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return nv;
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}
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// count the number of outgoing arcs, including reduced arcs
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static inline int count_out_without_del(const asg_t *g, uint32_t v)
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{
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uint32_t i, n, nv = asg_arc_n(g, v);
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const asg_arc_t *av = asg_arc_a(g, v);
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for (i = n = 0; i < nv; ++i)
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if (!av[i].del) ++n;
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return n;
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}
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void debug_info_of_specfic_read(char* name, ma_hit_t_alloc* sources,
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ma_hit_t_alloc* reverse_sources, int id, char* fun);
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void build_string_graph_without_clean(int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, long long n_read, uint64_t* readLen,
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long long mini_overlap_length, long long max_hang_length,
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long long clean_round, float min_ovlp_drop_ratio, float max_ovlp_drop_ratio,
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float corase_ovlp_drop_ratio, char* output_file_name, long long bubble_dist, int read_graph,
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int write);
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#endif
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