mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
Merge branch 'chain-tune' into merge2
This commit is contained in:
Heng Li
443
Hash_Table.h
443
Hash_Table.h
@@ -1,13 +1,6 @@
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#ifndef __HASHTABLE__
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#define __HASHTABLE__
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#include "khash.h"
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#include "kmer.h"
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KHASH_MAP_INIT_INT64(COUNT64, int)
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typedef khash_t(COUNT64) Count_Table;
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KHASH_MAP_INIT_INT64(POS64, uint64_t)
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typedef khash_t(POS64) Pos_Table;
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#include "htab.h"
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#define PREFIX_BITS 16
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#define MAX_SUFFIX_BITS 64
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@@ -37,26 +30,8 @@ typedef khash_t(POS64) Pos_Table;
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typedef struct
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{
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volatile int lock;
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}Hash_table_spin_lock;
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typedef struct
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{
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Count_Table** sub_h;
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Hash_table_spin_lock* sub_h_lock;
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int prefix_bits;
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int suffix_bits;
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///number of subtable
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int size;
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uint64_t suffix_mode;
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uint64_t non_unique_k_mer;
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} Total_Count_Table;
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typedef struct
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{
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uint64_t offset;
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uint64_t readID;
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uint32_t offset;
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uint32_t readID:31, rev:1;
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} k_mer_pos;
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typedef struct
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@@ -70,17 +45,9 @@ typedef struct
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typedef struct
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{
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k_mer_pos_list* list;
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uint64_t size;
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uint64_t length;
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} k_mer_pos_list_alloc;
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typedef struct
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{
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int C_L[CIGAR_MAX_LENGTH];
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char C_C[CIGAR_MAX_LENGTH];
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int length;
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int C_L[CIGAR_MAX_LENGTH];
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char C_C[CIGAR_MAX_LENGTH];
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int length;
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} CIGAR;
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typedef struct
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@@ -97,407 +64,96 @@ typedef struct
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CIGAR cigar;
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} window_list;
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typedef struct
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{
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window_list* buffer;
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long long length;
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long long size;
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}window_list_alloc;
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int32_t length;
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int32_t size;
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} window_list_alloc;
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typedef struct
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{
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uint64_t* buffer;
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uint64_t length;
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uint64_t size;
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}Fake_Cigar;
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uint32_t length;
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uint32_t size;
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} Fake_Cigar;
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typedef struct
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{
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uint64_t x_id;
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uint32_t x_id;
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///the begining and end of the whole overlap
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uint64_t x_pos_s;
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uint64_t x_pos_e;
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uint64_t x_pos_strand;
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uint32_t x_pos_s;
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uint32_t x_pos_e;
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uint32_t x_pos_strand;
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uint64_t y_id;
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uint64_t y_pos_s;
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uint64_t y_pos_e;
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uint64_t y_pos_strand;
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uint32_t y_id;
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uint32_t y_pos_s;
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uint32_t y_pos_e;
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uint32_t y_pos_strand;
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uint64_t overlapLen;
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uint64_t shared_seed;
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uint64_t align_length;
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///uint64_t total_errors;
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uint32_t overlapLen;
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uint32_t shared_seed;
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uint32_t align_length;
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uint8_t is_match;
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uint8_t without_large_indel;
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uint64_t non_homopolymer_errors;
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int8_t strong;
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uint32_t non_homopolymer_errors;
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window_list* w_list;
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uint64_t w_list_size;
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uint64_t w_list_length;
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int8_t strong;
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uint32_t w_list_size;
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uint32_t w_list_length;
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Fake_Cigar f_cigar;
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window_list_alloc boundary_cigars;
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} overlap_region;
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typedef struct
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{
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overlap_region* list;
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uint64_t size;
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uint64_t length;
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///uint64_t mapped_overlaps_length;
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long long mapped_overlaps_length;
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int64_t mapped_overlaps_length;
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} overlap_region_alloc;
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typedef struct
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{
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///uint64_t offset;
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long long offset;
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///uint64_t self_offset;
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long long self_offset;
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uint64_t readID;
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uint8_t strand;
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uint32_t readID:31, strand:1;
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uint32_t offset, self_offset;
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} k_mer_hit;
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typedef struct
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{
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k_mer_hit node;
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uint64_t ID;
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} ElemType;
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typedef struct
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{
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ElemType* heap;
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uint64_t* index_i;
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int len;
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int MaxSize;
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} HeapSq;
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typedef struct
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{
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long long* score;
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long long* pre;
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long long* indels;
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long long* self_length;
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long long length;
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long long size;
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typedef struct {
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int32_t *score;
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int64_t *pre;
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int32_t *indels;
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int32_t *self_length;
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int64_t *tmp; // MUST BE 64-bit integer
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int64_t length;
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int64_t size;
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} Chain_Data;
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typedef struct
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{
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k_mer_hit* list;
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k_mer_hit* tmp;
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long long length;
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long long size;
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uint64_t foward_pos;
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uint64_t rc_pos;
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Chain_Data chainDP;
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} Candidates_list;
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typedef struct
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{
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Pos_Table** sub_h;
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Hash_table_spin_lock* sub_h_lock;
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int prefix_bits;
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int suffix_bits;
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///number of subtable
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int size;
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uint64_t suffix_mode;
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k_mer_pos* pos;
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uint64_t useful_k_mer;
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uint64_t total_occ;
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uint64_t* k_mer_index;
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} Total_Pos_Table;
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inline uint64_t mod_d(uint64_t h_key, uint64_t low_key, uint64_t d)
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{
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uint64_t result = (h_key >> 32) % d;
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result = ((result << 32) + (h_key & (uint64_t)0xffffffff)) % d;
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result = ((result << 32) + (low_key >> 32)) % d;
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result = ((result << 32) + (low_key & (uint64_t)0xffffffff)) % d;
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return result;
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}
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////suffix_bits = 64 in default
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inline int recover_hash_code(uint64_t sub_ID, uint64_t sub_key, Hash_code* code,
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uint64_t suffix_mode, int suffix_bits, int k)
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{
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uint64_t h_key, low_key;
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h_key = low_key = 0;
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low_key = sub_ID << SAFE_SHIFT(suffix_bits);
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low_key = low_key | sub_key;
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h_key = sub_ID >> (64 - suffix_bits);
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code->x[0] = code->x[1] = 0;
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uint64_t mask = ALL >> (64 - k);
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code->x[0] = low_key & mask;
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code->x[1] = h_key << (64 - k);
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code->x[1] = code->x[1] | (low_key >> SAFE_SHIFT(k));
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return 1;
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}
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///inline int get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, Total_Count_Table* TCB, Hash_code* code, int k)
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inline int get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, uint64_t suffix_mode, int suffix_bits,
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Hash_code* code, int k)
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{
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uint64_t h_key, low_key;
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///k might be 64，so it is unsafe
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///low_key = code->x[0] | (code->x[1] << k);
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low_key = code->x[0] | (code->x[1] << SAFE_SHIFT(k));
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//k cannot be 0, so this shift is safe
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h_key = code->x[1] >> (64 - k);
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if(mod_d(h_key, low_key, MODE_VALUE) > 3)
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{
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return 0;
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}
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uint64_t sub_ID = (low_key >> SAFE_SHIFT(suffix_bits)) | (h_key << (64 - suffix_bits));
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uint64_t sub_key = (low_key & suffix_mode);
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*get_sub_ID = sub_ID;
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*get_sub_key = sub_key;
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return 1;
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}
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inline int insert_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
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{
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uint64_t sub_ID, sub_key;
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if(!get_sub_table(&sub_ID, &sub_key, TCB->suffix_mode, TCB->suffix_bits, code, k))
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{
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return 0;
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}
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khint_t t;
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int absent;
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while (__sync_lock_test_and_set(&TCB->sub_h_lock[sub_ID].lock, 1))
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{
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while (TCB->sub_h_lock[sub_ID].lock);
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}
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t = kh_put(COUNT64, TCB->sub_h[sub_ID], sub_key, &absent);
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if (absent)
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{
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kh_value(TCB->sub_h[sub_ID], t) = 1;
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}
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else
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{
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//kh_value(TCB->sub_h[sub_ID], t) = kh_value(TCB->sub_h[sub_ID], t) + 1;
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kh_value(TCB->sub_h[sub_ID], t)++;
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}
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__sync_lock_release(&TCB->sub_h_lock[sub_ID].lock);
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return 1;
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}
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inline int get_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
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{
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uint64_t sub_ID, sub_key;
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if(!get_sub_table(&sub_ID, &sub_key, TCB->suffix_mode, TCB->suffix_bits, code, k))
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{
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return 0;
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}
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khint_t t;
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///query hash table，key is k
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t = kh_get(COUNT64, TCB->sub_h[sub_ID], sub_key);
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|
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if (t != kh_end(TCB->sub_h[sub_ID]))
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{
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return kh_value(TCB->sub_h[sub_ID], t);
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}
|
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else
|
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{
|
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return 0;
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}
|
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|
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|
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}
|
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inline uint64_t get_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k, uint64_t* r_sub_ID)
|
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{
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uint64_t sub_ID, sub_key;
|
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if(!get_sub_table(&sub_ID, &sub_key, PCB->suffix_mode, PCB->suffix_bits, code, k))
|
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{
|
||||
return (uint64_t)-1;
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}
|
||||
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khint_t t;
|
||||
|
||||
///query hash table，key is k
|
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t = kh_get(POS64, PCB->sub_h[sub_ID], sub_key);
|
||||
|
||||
if (t != kh_end(PCB->sub_h[sub_ID]))
|
||||
{
|
||||
*r_sub_ID = sub_ID;
|
||||
return kh_value(PCB->sub_h[sub_ID], t);
|
||||
}
|
||||
else
|
||||
{
|
||||
return (uint64_t)-1;
|
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}
|
||||
|
||||
|
||||
}
|
||||
|
||||
inline uint64_t count_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k)
|
||||
{
|
||||
uint64_t sub_ID;
|
||||
uint64_t ret = get_Total_Pos_Table(PCB, code, k, &sub_ID);
|
||||
if(ret != (uint64_t)-1)
|
||||
{
|
||||
return PCB->k_mer_index[ret + 1] - PCB->k_mer_index[ret];
|
||||
}
|
||||
else
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
inline uint64_t locate_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, k_mer_pos** list, int k, uint64_t* r_sub_ID)
|
||||
{
|
||||
uint64_t ret = get_Total_Pos_Table(PCB, code, k, r_sub_ID);
|
||||
if(ret != (uint64_t)-1)
|
||||
{
|
||||
*list = PCB->k_mer_index[ret] + PCB->pos;
|
||||
return PCB->k_mer_index[ret + 1] - PCB->k_mer_index[ret];
|
||||
}
|
||||
else
|
||||
{
|
||||
*list = NULL;
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
|
||||
int cmp_k_mer_pos(const void * a, const void * b);
|
||||
|
||||
|
||||
inline uint64_t insert_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k, uint64_t readID, uint64_t pos)
|
||||
{
|
||||
k_mer_pos* list;
|
||||
int flag = 0;
|
||||
uint64_t sub_ID;
|
||||
uint64_t occ = locate_Total_Pos_Table(PCB, code, &list, k, &sub_ID);
|
||||
|
||||
if (occ)
|
||||
{
|
||||
|
||||
while (__sync_lock_test_and_set(&PCB->sub_h_lock[sub_ID].lock, 1))
|
||||
{
|
||||
while (PCB->sub_h_lock[sub_ID].lock);
|
||||
}
|
||||
|
||||
if (list[0].offset + 1 < occ)
|
||||
{
|
||||
list[0].offset++;
|
||||
list[list[0].offset].readID = readID;
|
||||
///list[list[0].offset].readID = readID|direction;
|
||||
list[list[0].offset].offset = pos;
|
||||
}
|
||||
else
|
||||
{
|
||||
list[0].readID = readID;
|
||||
///list[0].readID = readID|direction;
|
||||
list[0].offset = pos;
|
||||
flag = 1;
|
||||
}
|
||||
|
||||
__sync_lock_release(&PCB->sub_h_lock[sub_ID].lock);
|
||||
|
||||
//if all pos has been saved, it is safe to sort
|
||||
if (flag && occ>1)
|
||||
{
|
||||
qsort(list, occ, sizeof(k_mer_pos), cmp_k_mer_pos);
|
||||
}
|
||||
|
||||
|
||||
return 1;
|
||||
}
|
||||
else
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
void init_Total_Count_Table(int k, Total_Count_Table* TCB);
|
||||
void init_Total_Pos_Table(Total_Pos_Table* TCB, Total_Count_Table* pre_TCB);
|
||||
void destory_Total_Count_Table(Total_Count_Table* TCB);
|
||||
|
||||
void init_Count_Table(Count_Table** table);
|
||||
void init_Pos_Table(Count_Table** pre_table, Pos_Table** table);
|
||||
void destory_Total_Pos_Table(Total_Pos_Table* TCB);
|
||||
void write_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name);
|
||||
int load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name);
|
||||
|
||||
|
||||
|
||||
void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k_mer_min_freq, int k_mer_max_freq);
|
||||
|
||||
void init_Candidates_list(Candidates_list* l);
|
||||
void clear_Candidates_list(Candidates_list* l);
|
||||
void destory_Candidates_list(Candidates_list* l);
|
||||
|
||||
|
||||
void init_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list);
|
||||
void destory_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list);
|
||||
void clear_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list);
|
||||
void append_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list, k_mer_pos* n_list, uint64_t n_length,
|
||||
uint64_t n_end_pos, uint8_t n_direction);
|
||||
|
||||
|
||||
|
||||
void merge_k_mer_pos_list_alloc_heap_sort(k_mer_pos_list_alloc* list, Candidates_list* candidates, HeapSq* HBT);
|
||||
|
||||
void Init_Heap(HeapSq* HBT);
|
||||
void destory_Heap(HeapSq* HBT);
|
||||
void clear_Heap(HeapSq* HBT);
|
||||
|
||||
void init_overlap_region_alloc(overlap_region_alloc* list);
|
||||
void clear_overlap_region_alloc(overlap_region_alloc* list);
|
||||
void destory_overlap_region_alloc(overlap_region_alloc* list);
|
||||
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 error_threshold);
|
||||
|
||||
|
||||
|
||||
void overlap_region_sort_y_id(overlap_region *a, long long n);
|
||||
|
||||
|
||||
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, int add_beg_end);
|
||||
|
||||
|
||||
|
||||
void init_fake_cigar(Fake_Cigar* x);
|
||||
void destory_fake_cigar(Fake_Cigar* x);
|
||||
void clear_fake_cigar(Fake_Cigar* x);
|
||||
@@ -505,14 +161,14 @@ void add_fake_cigar(Fake_Cigar* x, uint32_t gap_site, int32_t gap_shift);
|
||||
void resize_fake_cigar(Fake_Cigar* x, uint64_t 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)
|
||||
|
||||
static 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 < (long long)o->length; i++)
|
||||
{
|
||||
@@ -524,7 +180,7 @@ inline long long y_start_offset(long long x_start, Fake_Cigar* o)
|
||||
|
||||
if(i == 0 || i == (long long)o->length)
|
||||
{
|
||||
fprintf(stderr, "ERROR\n");
|
||||
fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
|
||||
exit(0);
|
||||
}
|
||||
|
||||
@@ -532,24 +188,11 @@ inline long long y_start_offset(long long x_start, Fake_Cigar* o)
|
||||
return get_fake_gap_shift(o, i - 1);
|
||||
}
|
||||
|
||||
inline void print_fake_gap(Fake_Cigar* o)
|
||||
{
|
||||
long long i;
|
||||
for (i = 0; i < (long long)o->length; i++)
|
||||
{
|
||||
fprintf(stderr, "**i: %lld, gap_pos_in_x: %d, gap_shift: %d\n",
|
||||
i, get_fake_gap_pos(o, i),
|
||||
get_fake_gap_shift(o, i));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
void resize_Chain_Data(Chain_Data* x, long long size);
|
||||
void init_window_list_alloc(window_list_alloc* x);
|
||||
void clear_window_list_alloc(window_list_alloc* x);
|
||||
void destory_window_list_alloc(window_list_alloc* x);
|
||||
void resize_window_list_alloc(window_list_alloc* x, long long size);
|
||||
void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* result,
|
||||
double band_width_threshold, int max_skip, int x_readLen, int y_readLen);
|
||||
void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* result, double band_width_threshold, int max_skip, int x_readLen, int y_readLen);
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
Reference in New Issue
Block a user