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final DP-based assembly

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This commit is contained in:
Haoyu Cheng
2019-11-13 20:18:11 -05:00
parent d6c6a1fa11
commit ada03ea388
22 changed files with 19432 additions and 1178 deletions
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Hash_Table.h
+127 -11
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@@ -17,23 +17,23 @@ typedef khash_t(POS64) Pos_Table;
///#define THRESHOLD 14
#define WINDOW 375
#define WINDOW_BOUNDARY 150
//#define WINDOW_BOUNDARY 150
#define WINDOW_BOUNDARY 375
///for one side, the first or last WINDOW_UNCORRECT_SINGLE_SIDE_BOUNDARY bases should not be corrected
#define WINDOW_UNCORRECT_SINGLE_SIDE_BOUNDARY 25
#define THRESHOLD 15
#define THRESHOLD_RATE 0.04
#define OVERLAP_THRESHOLD 0.9
#define TAIL_LENGTH int(1/THRESHOLD_RATE)
///#define OVERLAP_THRESHOLD 0.9
#define OVERLAP_THRESHOLD_FILTER 0.9
#define WINDOW_MAX_SIZE WINDOW + TAIL_LENGTH + 3
#define THRESHOLD_MAX_SIZE 31
/**
#define WINDOW 500
#define THRESHOLD 15
#define THRESHOLD_RATE 0.03
#define OVERLAP_THRESHOLD 0.95
**/
#define GROUP_SIZE 4
///最长是10M10D10M10D10M这种
#define CIGAR_MAX_LENGTH THRESHOLD*2+2
///#define CIGAR_MAX_LENGTH THRESHOLD*2+2
#define CIGAR_MAX_LENGTH 31*2+4
typedef struct
{
@@ -92,12 +92,21 @@ typedef struct
int y_start;
int extra_begin;
int extra_end;
int error_threshold;
///int y_pre_start;
///error小于等于0都要重新算
int error;
CIGAR cigar;
} window_list;
typedef struct
{
uint64_t* buffer;
uint64_t length;
uint64_t size;
}Fake_Cigar;
typedef struct
{
uint64_t x_id;
@@ -113,10 +122,15 @@ typedef struct
uint64_t shared_seed;
uint64_t align_length;
///uint64_t total_errors;
uint8_t is_match;
uint64_t non_homopolymer_errors;
window_list* w_list;
uint64_t w_list_size;
uint64_t w_list_length;
int8_t strong;
Fake_Cigar f_cigar;
} overlap_region;
@@ -125,6 +139,8 @@ typedef struct
overlap_region* list;
uint64_t size;
uint64_t length;
///uint64_t mapped_overlaps_length;
long long mapped_overlaps_length;
} overlap_region_alloc;
typedef struct
@@ -153,7 +169,15 @@ typedef struct
int MaxSize;
} HeapSq;
typedef struct
{
long long* score;
long long* pre;
long long* indels;
long long* self_length;
long long length;
long long size;
} Chain_Data;
typedef struct
{
@@ -163,6 +187,7 @@ typedef struct
long long size;
uint64_t foward_pos;
uint64_t rc_pos;
Chain_Data chainDP;
} Candidates_list;
typedef struct
@@ -206,6 +231,23 @@ inline uint64_t mod_d(uint64_t h_key, uint64_t low_key, uint64_t d)
return result;
}
inline int if_k_mer_available(Hash_code* code, int k)
{
uint64_t h_key, low_key;
///k有可能是64，所以可能会有问题
///low_key = code->x[0] | (code->x[1] << k);
low_key = code->x[0] | (code->x[1] << SAFE_SHIFT(k));
//k不可能为0, 所以这个右移不会有问题
h_key = code->x[1] >> (64 - k);
if(mod_d(h_key, low_key, MODE_VALUE) > 3)
{
return 0;
}
return 1;
}
///inline int get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, Total_Count_Table* TCB, Hash_code* code, int k)
@@ -458,16 +500,84 @@ void append_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp
void calculate_overlap_region(Candidates_list* candidates, overlap_region_alloc* overlap_list,
uint64_t readID, uint64_t readLength, All_reads* R_INF);
void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error,
int extra_begin, int extra_end);
int extra_begin, int extra_end, int error_threshold);
void insert_kv_list_to_candidates(k_v* list, long long occ, long long y_id, long long y_offset, long long y_strand,
Candidates_list* candidates);
void overlap_region_sort_y_id(overlap_region *a, long long n);
void calculate_inexact_overlap_region(Candidates_list* candidates, overlap_region_alloc* overlap_list,
uint64_t readID, uint64_t readLength, All_reads* R_INF);
void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list,
uint64_t readID, uint64_t readLength, All_reads* R_INF, double band_width_threshold);
static const char LogTable256[256] = {
#define LT(n) n, n, n, n, n, n, n, n, n, n, n, n, n, n, n, n
-1, 0, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3,
LT(4), LT(5), LT(5), LT(6), LT(6), LT(6), LT(6),
LT(7), LT(7), LT(7), LT(7), LT(7), LT(7), LT(7), LT(7)
};
static inline int ilog2_32(uint32_t v)
{
uint32_t t, tt;
if ((tt = v>>16)) return (t = tt>>8) ? 24 + LogTable256[t] : 16 + LogTable256[tt];
return (t = v>>8) ? 8 + LogTable256[t] : LogTable256[v];
}
void init_fake_cigar(Fake_Cigar* x);
void destory_fake_cigar(Fake_Cigar* x);
void clear_fake_cigar(Fake_Cigar* x);
void add_fake_cigar(Fake_Cigar* x, uint32_t gap_site, int32_t gap_shift);
void resize_fake_cigar(Fake_Cigar* x, long long size);
int get_fake_gap_pos(Fake_Cigar* x, int index);
int get_fake_gap_shift(Fake_Cigar* x, int index);
inline long long y_start_offset(long long x_start, Fake_Cigar* o)
{
if(x_start == get_fake_gap_pos(o, o->length - 1))
{
return get_fake_gap_shift(o, o->length - 1);
}
long long i;
for (i = 0; i < o->length; i++)
{
if(x_start < get_fake_gap_pos(o, i))
{
break;
}
}
if(i == 0 || i == o->length)
{
fprintf(stderr, "ERROR\n");
exit(0);
}
///note here return i - 1
return get_fake_gap_shift(o, i - 1);
}
inline void print_fake_gap(Fake_Cigar* o)
{
long long i;
for (i = 0; i < o->length; i++)
{
fprintf(stderr, "**i: %d, gap_pos_in_x: %d, gap_shift: %d\n",
i, get_fake_gap_pos(o, i),
get_fake_gap_shift(o, i));
}
}
@@ -585,4 +695,10 @@ void debug_mode(uint64_t d, uint64_t thread_ID, uint64_t thread_num);
/********************************for debug***************************************/
void merge_Candidates_list_version(Candidates_list* l, k_mer_pos* n_list, uint64_t n_lengh, uint64_t end_pos, int strand);
void sort_candidates(Candidates_list* candidates, long long readID,
overlap_region_alloc* overlap_list, All_reads* R_INF);
void append_overlap_region_alloc_from_existing(overlap_region_alloc* list, overlap_region* tmp, All_reads* R_INF);
int cmp_by_x_pos_s(const void * a, const void * b);
void resize_Chain_Data(Chain_Data* x, long long size);
#endif