mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-11 04:20:55 +08:00
Reduce memory requirement
This commit is contained in:
Haoyu Cheng
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+96
-10
@@ -48,6 +48,7 @@ void* Perform_Counting(void* arg)
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for (i = 0; i < curr_sub_block.num; i++)
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{
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///forward strand
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init_HPC_seq(&HPC_read, curr_sub_block.read[i].seq.s, curr_sub_block.read[i].seq.l);
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init_Hash_code(&k_code);
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@@ -81,6 +82,43 @@ void* Perform_Counting(void* arg)
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}
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/**
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///reverse complement strand
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reverse_complement(curr_sub_block.read[i].seq.s, curr_sub_block.read[i].seq.l);
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init_HPC_seq(&HPC_read, curr_sub_block.read[i].seq.s, curr_sub_block.read[i].seq.l);
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init_Hash_code(&k_code);
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avalible_k = 0;
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while ((code = get_HPC_code(&HPC_read)) != 6)
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{
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if(code < 4)
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{
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k_mer_append(&k_code,code,k_mer_length);
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avalible_k++;
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if (avalible_k>=k_mer_length)
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{
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///插入
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if(insert_Total_Count_Table(&TCB, &k_code, k_mer_length))
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{
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select_k_mer_number++;
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}
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k_mer_number++;
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}
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}
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else
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{
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avalible_k = 0;
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init_Hash_code(&k_code);
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}
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}
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**/
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}
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@@ -117,7 +155,6 @@ void* Build_hash_table(void* arg)
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int avalible_k = 0;
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char* dest;
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while (file_flag != 0)
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{
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@@ -128,13 +165,55 @@ void* Build_hash_table(void* arg)
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for (i = 0; i < curr_sub_block.num; i++)
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{
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dest = R_INF.read+R_INF.index[curr_sub_block.read[i].ID];
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memcpy(dest, curr_sub_block.read[i].seq.s, curr_sub_block.read[i].seq.l);
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///forward strand
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init_HPC_seq(&HPC_read, curr_sub_block.read[i].seq.s, curr_sub_block.read[i].seq.l);
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init_Hash_code(&k_code);
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dest = R_INF.name+R_INF.name_index[curr_sub_block.read[i].ID];
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memcpy(dest, curr_sub_block.read[i].name.s, curr_sub_block.read[i].name.l);
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avalible_k = 0;
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HPC_base = 0;
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while ((code = get_HPC_code(&HPC_read)) != 6)
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{
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if(code < 4)
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{
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k_mer_append(&k_code,code,k_mer_length);
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avalible_k++;
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if (avalible_k>=k_mer_length)
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{
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///选取的k-mer满足两个要求
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///1. hash(k-mer) % 101 <= 3
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///2. occ(k-mer)要满足范围
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///TCB表中的元素仅满足第一个要求，而PCB表中的元素满足两个要求
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///所以如果当前k-mer在PCB表中存在，则他的位置一定要加入到候选位置中去
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///insert_Total_Pos_Table(&PCB, &k_code, k_mer_length, curr_sub_block.read[i].ID, HPC_base - k_mer_length + 1, FORWARD);
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insert_Total_Pos_Table(&PCB, &k_code, k_mer_length,
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curr_sub_block.read[i].ID, HPC_base - k_mer_length + 1);
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}
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}
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else
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{
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avalible_k = 0;
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init_Hash_code(&k_code);
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}
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HPC_base++;
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}
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///load read
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compress_base(Get_READ(R_INF, curr_sub_block.read[i].ID),
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curr_sub_block.read[i].seq.s, curr_sub_block.read[i].seq.l,
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&R_INF.N_site[curr_sub_block.read[i].ID], HPC_read.N_occ);
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memcpy(R_INF.name+R_INF.name_index[curr_sub_block.read[i].ID],
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curr_sub_block.read[i].name.s, curr_sub_block.read[i].name.l);
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/**
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///reverse complement strand
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reverse_complement(curr_sub_block.read[i].seq.s, curr_sub_block.read[i].seq.l);
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init_HPC_seq(&HPC_read, curr_sub_block.read[i].seq.s, curr_sub_block.read[i].seq.l);
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init_Hash_code(&k_code);
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@@ -158,7 +237,7 @@ void* Build_hash_table(void* arg)
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///TCB表中的元素仅满足第一个要求，而PCB表中的元素满足两个要求
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///所以如果当前k-mer在PCB表中存在，则他的位置一定要加入到候选位置中去
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insert_Total_Pos_Table(&PCB, &k_code, k_mer_length,
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curr_sub_block.read[i].ID, HPC_base - k_mer_length + 1);
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curr_sub_block.read[i].ID, HPC_base - k_mer_length + 1, REVERSE_COMPLEMENT);
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}
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}
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@@ -170,8 +249,7 @@ void* Build_hash_table(void* arg)
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HPC_base++;
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}
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**/
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}
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@@ -269,6 +347,7 @@ void Build_hash_table_multiple_thr()
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Traverse_Counting_Table(&TCB, &PCB, k_mer_min_freq, k_mer_max_freq);
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fprintf(stdout, "%-30s%18.2f\n\n", "Traverse time:", Get_T() - T_start_time);
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fflush(stdout);
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@@ -408,6 +487,9 @@ void verify_Position_hash_table()
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k_mer_pos* list;
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uint64_t sub_ID;
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UC_Read g_read;
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init_UC_Read(&g_read);
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fprintf(stdout, "Start Verifying Position Table...\n");
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while (get_read(seq))
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@@ -419,9 +501,13 @@ void verify_Position_hash_table()
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fprintf(stderr, "seq error\n");
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}
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if(memcmp(seq->seq.s, Get_READ(R_INF, read_number), seq->seq.l))
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recover_UC_Read(&g_read, &R_INF, read_number);
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if(memcmp(seq->seq.s, g_read.seq, seq->seq.l))
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{
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fprintf(stderr, "seq error\n");
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fprintf(stderr, "\nseq error ID: %llu, length: %llu\n",read_number, seq->seq.l);
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}
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if (seq->name.l
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@@ -1,6 +1,9 @@
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#ifndef __ASSEMBLY__
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#define __ASSEMBLY__
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#define FORWARD 0
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#define REVERSE_COMPLEMENT (0x8000000000000000)
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void Counting_multiple_thr();
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@@ -234,6 +234,7 @@ inline uint64_t locate_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, k_
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int cmp_k_mer_pos(const void * a, const void * b);
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//inline uint64_t insert_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k, uint64_t readID, uint64_t pos, uint64_t direction)
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inline uint64_t insert_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k, uint64_t readID, uint64_t pos)
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{
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k_mer_pos* list;
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@@ -253,11 +254,13 @@ inline uint64_t insert_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, in
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{
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list[0].offset++;
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list[list[0].offset].readID = readID;
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///list[list[0].offset].readID = readID|direction;
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list[list[0].offset].offset = pos;
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}
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else
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{
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list[0].readID = readID;
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///list[0].readID = readID|direction;
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list[0].offset = pos;
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flag = 1;
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}
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+157
-1
@@ -27,6 +27,7 @@ void init_All_reads(All_reads* r)
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r->index = (uint64_t*)malloc(sizeof(uint64_t)*r->index_size);
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r->index[0] = 0;
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r->read = NULL;
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r->N_site = NULL;
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r->total_reads_bases = 0;
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@@ -57,14 +58,141 @@ inline void insert_read(All_reads* r, kstring_t* read, kstring_t* name)
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r->name_index = (uint64_t*)realloc(r->name_index,sizeof(uint64_t)*(r->name_index_size));
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}
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r->index[r->total_reads] = r->index[r->total_reads-1] + read->l;
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//r->index[r->total_reads] = r->index[r->total_reads-1] + read->l/4 + 1;
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r->name_index[r->total_reads] = r->name_index[r->total_reads-1] + name->l;
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}
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void malloc_All_reads(All_reads* r)
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{
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r->read = (char*)malloc(sizeof(char)*r->total_reads_bases);
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///必须加r->total_reads
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r->read = (uint8_t*)malloc(sizeof(uint8_t)*(r->total_reads_bases/4 + r->total_reads + 5));
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r->name = (char*)malloc(sizeof(char)*r->total_name_length);
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r->N_site = (uint64_t**)malloc(sizeof(uint64_t*)*r->total_reads);
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}
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void init_UC_Read(UC_Read* r)
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{
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r->length = 0;
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r->size = 0;
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r->seq = NULL;
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if (bit_t_seq_table[0][0] == 0)
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{
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uint64_t i = 0;
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for (i = 0; i < 256; i++)
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{
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bit_t_seq_table[i][0] = s_H[((i >> 6)&(uint64_t)3)];
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bit_t_seq_table[i][1] = s_H[((i >> 4)&(uint64_t)3)];
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bit_t_seq_table[i][2] = s_H[((i >> 2)&(uint64_t)3)];
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bit_t_seq_table[i][3] = s_H[(i&(uint64_t)3)];
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}
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}
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}
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void recover_UC_Read(UC_Read* r, All_reads* R_INF, uint64_t ID)
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{
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r->length = Get_READ_LENGTH((*R_INF), ID);
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uint8_t* src = Get_READ((*R_INF), ID);
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if (r->length + 4 > r->size)
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{
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r->size = r->length + 4;
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r->seq = (char*)realloc(r->seq,sizeof(char)*(r->size));
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}
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uint64_t i = 0;
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while (i < r->length)
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{
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memcpy(r->seq+i, bit_t_seq_table[src[i>>2]], 4);
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i = i + 4;
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}
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if (R_INF->N_site[ID])
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{
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for (i = 1; i <= R_INF->N_site[ID][0]; i++)
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{
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r->seq[R_INF->N_site[ID][i]] = 'N';
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}
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}
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}
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#define COMPRESS_BASE {c = seq_nt6_table[src[i]];\
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if (c >= 4)\
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{\
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c = 0;\
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(*N_site_lis)[N_site_i] = i;\
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N_site_i++;\
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}\
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i++;}\
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void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_lis, uint64_t N_site_occ)
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{
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if (N_site_occ)
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{
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(*N_site_lis) = (uint64_t*)malloc(sizeof(uint64_t)*(N_site_occ + 1));
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(*N_site_lis)[0] = N_site_occ;
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}
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else
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{
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(*N_site_lis) = NULL;
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}
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uint64_t i = 0;
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uint64_t N_site_i = 1;
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uint64_t dest_i = 0;
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uint8_t tmp = 0;
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uint8_t c = 0;
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while (i + 4 <= src_l)
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{
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tmp = 0;
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COMPRESS_BASE;
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tmp = tmp | (c<<6);
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COMPRESS_BASE;
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tmp = tmp | (c<<4);
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COMPRESS_BASE;
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tmp = tmp | (c<<2);
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COMPRESS_BASE;
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tmp = tmp | c;
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dest[dest_i] = tmp;
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dest_i++;
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}
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//最多还剩3个字符
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uint64_t shift = 6;
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if (i < src_l)
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{
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tmp = 0;
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while (i < src_l)
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{
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COMPRESS_BASE;
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tmp = tmp | (c << shift);
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shift = shift -2;
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}
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dest[dest_i] = tmp;
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dest_i++;
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}
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}
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void init_kseq(char* file)
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@@ -348,6 +476,34 @@ int get_reads_mul_thread(R_buffer_block* curr_sub_block)
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void reverse_complement(char* pattern, uint64_t length)
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{
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int i = 0;
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uint64_t end = length / 2;
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char k;
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uint64_t index;
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for (i = 0; i < end; i++)
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{
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index = length - i - 1;
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k = pattern[index];
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pattern[index] = RC_CHAR(pattern[i]);
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pattern[i] = RC_CHAR(k);
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}
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if(length&(uint64_t)1)
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{
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pattern[end] = RC_CHAR(pattern[end]);
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}
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}
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void Counting_block()
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{
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+44
-3
@@ -16,13 +16,41 @@
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#define IS_EMPTY(buffer) ((buffer.num == 0)?1:0)
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#define Get_READ_LENGTH(R_INF, ID) (R_INF.index[ID+1] - R_INF.index[ID])
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#define Get_NAME_LENGTH(R_INF, ID) (R_INF.name_index[ID+1] - R_INF.name_index[ID])
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#define Get_READ(R_INF, ID) (R_INF.read + R_INF.index[ID])
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#define Get_NAME(R_INF, ID) (R_INF.name + R_INF.name_index[ID])
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#define Get_READ(R_INF, ID) R_INF.read + (R_INF.index[ID]>>2) + ID
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#define Get_NAME(R_INF, ID) R_INF.name + R_INF.name_index[ID]
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KSEQ_INIT(gzFile, gzread)
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static uint8_t seq_nt6_table[256] = {
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5
|
||||
};
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||||
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static char bit_t_seq_table[256][4] = {0};
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static char s_H[4] = {'A', 'C', 'G', 'T'};
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||||
static char rc_Table[4] = {'T', 'G', 'C', 'A'};
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||||
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||||
#define RC_CHAR(x) rc_Table[seq_nt6_table[(uint8_t)x]]
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||||
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||||
|
||||
void init_kseq(char* file);
|
||||
void destory_kseq();
|
||||
int get_read(kseq_t *s);
|
||||
@@ -31,7 +59,8 @@ int get_read(kseq_t *s);
|
||||
|
||||
typedef struct
|
||||
{
|
||||
char* read;
|
||||
uint64_t** N_site;
|
||||
uint8_t* read;
|
||||
char* name;
|
||||
uint64_t* index;
|
||||
uint64_t index_size;
|
||||
@@ -64,11 +93,23 @@ typedef struct
|
||||
int all_read_end;
|
||||
} R_buffer;
|
||||
|
||||
|
||||
typedef struct
|
||||
{
|
||||
char* seq;
|
||||
long long length;
|
||||
long long size;
|
||||
} UC_Read;
|
||||
|
||||
void init_R_buffer(int thread_num);
|
||||
void init_All_reads(All_reads* r);
|
||||
void* input_reads_muti_threads(void*);
|
||||
void init_R_buffer_block(R_buffer_block* curr_sub_block);
|
||||
int get_reads_mul_thread(R_buffer_block* curr_sub_block);
|
||||
void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_lis, uint64_t N_site_occ);
|
||||
void init_UC_Read(UC_Read* r);
|
||||
void recover_UC_Read(UC_Read* r, All_reads* R_INF, uint64_t ID);
|
||||
void reverse_complement(char* pattern, uint64_t length);
|
||||
|
||||
void Counting_block();
|
||||
void destory_R_buffer_block(R_buffer_block* curr_sub_block);
|
||||
|
||||
@@ -6,6 +6,7 @@ void init_HPC_seq(HPC_seq* seq, char* str, long long l)
|
||||
{
|
||||
seq->i = 0;
|
||||
seq->l = l;
|
||||
seq->N_occ = 0;
|
||||
seq->str = str;
|
||||
}
|
||||
|
||||
|
||||
@@ -2,29 +2,13 @@
|
||||
#define __KMER__
|
||||
#include "Process_Read.h"
|
||||
|
||||
#define ALL (0xffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff)
|
||||
///#define ALL (0xffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff)
|
||||
#define ALL (0xffffffffffffffff)
|
||||
|
||||
#define SAFE_SHIFT(k) k & ((k < 64)?ALL:0)
|
||||
|
||||
|
||||
static unsigned char seq_nt6_table[256] = {
|
||||
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
|
||||
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5
|
||||
};
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -44,6 +28,7 @@ typedef struct
|
||||
char* str;
|
||||
long long l;
|
||||
long long i;
|
||||
long long N_occ;
|
||||
|
||||
} HPC_seq;
|
||||
|
||||
@@ -53,17 +38,23 @@ inline uint64_t get_HPC_code(HPC_seq* seq)
|
||||
|
||||
if(seq->i < seq ->l)
|
||||
{
|
||||
char code = seq->str[seq->i];
|
||||
uint8_t code = seq_nt6_table[(uint8_t)seq->str[seq->i]];
|
||||
|
||||
for (; seq->i < seq->l; seq->i++)
|
||||
{
|
||||
if (seq->str[seq->i] != code)
|
||||
///统计N的个数
|
||||
if (seq_nt6_table[(uint8_t)seq->str[seq->i]] >= 4)
|
||||
{
|
||||
seq->N_occ++;
|
||||
}
|
||||
|
||||
if (seq_nt6_table[(uint8_t)seq->str[seq->i]] != code)
|
||||
{
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
return (uint64_t)seq_nt6_table[(uint8_t)code];
|
||||
return (uint64_t)code;
|
||||
}
|
||||
else
|
||||
{
|
||||
|
||||
Reference in New Issue
Block a user