mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-30 08:38:11 +08:00
removed hifiasm hash table index
This commit is contained in:
Heng Li
+67
-498
@@ -11,426 +11,13 @@
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#include "Output.h"
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#include "htab.h"
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Total_Count_Table TCB;
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Total_Pos_Table PCB;
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void *ha_flt_tab;
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void *ha_idx;
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All_reads R_INF;
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pthread_mutex_t statistics;
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void* Perform_Counting(void* arg)
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{
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int i = 0;
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HPC_seq HPC_read;
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R_buffer_block curr_sub_block;
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init_R_buffer_block(&curr_sub_block);
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long long read_number = 0;
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long long select_k_mer_number = 0 ;
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long long k_mer_number = 0 ;
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int file_flag = 1;
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uint64_t code;
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uint64_t end_pos;
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Hash_code k_code;
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int avalible_k = 0;
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while (file_flag != 0)
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{
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file_flag = get_reads_mul_thread(&curr_sub_block);
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read_number = read_number + curr_sub_block.num;
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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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avalible_k = 0;
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while ((code = get_HPC_code(&HPC_read, &end_pos)) != 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, asm_opt.k_mer_length);
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avalible_k++;
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if (avalible_k >= asm_opt.k_mer_length)
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{
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if(insert_Total_Count_Table(&TCB, &k_code, asm_opt.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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destory_R_buffer_block(&curr_sub_block);
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free(arg);
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return NULL;
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}
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void* Perform_Counting_non_first(void* arg)
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{
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int thr_ID = *((int*)arg);
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uint64_t i = 0;
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HPC_seq HPC_read;
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long long select_k_mer_number = 0 ;
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long long k_mer_number = 0 ;
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uint64_t code;
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uint64_t end_pos;
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Hash_code k_code;
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int avalible_k = 0;
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UC_Read g_read;
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init_UC_Read(&g_read);
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for (i = thr_ID; i < R_INF.total_reads; i = i + asm_opt.thread_num)
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{
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recover_UC_Read(&g_read, &R_INF, i);
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///forward strand
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init_HPC_seq(&HPC_read, g_read.seq, g_read.length);
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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, &end_pos)) != 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, asm_opt.k_mer_length);
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avalible_k++;
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if (avalible_k >= asm_opt.k_mer_length)
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{
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if(insert_Total_Count_Table(&TCB, &k_code, asm_opt.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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destory_UC_Read(&g_read);
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free(arg);
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return NULL;
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}
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void* Build_hash_table_non_first(void* arg)
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{
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int thr_ID = *((int*)arg);
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uint64_t i = 0;
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HPC_seq HPC_read;
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uint64_t code;
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uint64_t end_pos;
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///long long HPC_base;
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Hash_code k_code;
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int avalible_k = 0;
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UC_Read g_read;
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init_UC_Read(&g_read);
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for (i = thr_ID; i < R_INF.total_reads; i = i + asm_opt.thread_num)
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{
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recover_UC_Read(&g_read, &R_INF, i);
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///forward strand
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init_HPC_seq(&HPC_read, g_read.seq, g_read.length);
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init_Hash_code(&k_code);
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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, &end_pos)) != 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, asm_opt.k_mer_length);
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avalible_k++;
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if (avalible_k >= asm_opt.k_mer_length)
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{
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///there are two requirements
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///1. hash(k-mer)
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///2. occ(k-mer)
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///TCB just meet the first requirement，while PCB needs to meet both of them
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insert_Total_Pos_Table(&PCB, &k_code, asm_opt.k_mer_length, i, end_pos);
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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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destory_UC_Read(&g_read);
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free(arg);
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return NULL;
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}
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void* Build_hash_table(void* arg)
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{
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int i = 0;
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HPC_seq HPC_read;
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R_buffer_block curr_sub_block;
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init_R_buffer_block(&curr_sub_block);
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int file_flag = 1;
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uint64_t code;
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uint64_t end_pos;
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///long long HPC_base;
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Hash_code k_code;
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int avalible_k = 0;
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while (file_flag != 0)
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{
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file_flag = get_reads_mul_thread(&curr_sub_block);
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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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avalible_k = 0;
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///HPC_base = 0;
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while ((code = get_HPC_code(&HPC_read, &end_pos)) != 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, asm_opt.k_mer_length);
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avalible_k++;
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if (avalible_k >= asm_opt.k_mer_length)
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{
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///there are two requirements
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///1. hash(k-mer)
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///2. occ(k-mer)
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///TCB just meet the first requirement，while PCB needs to meet both of them
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insert_Total_Pos_Table(&PCB, &k_code, asm_opt.k_mer_length, curr_sub_block.read[i].ID, end_pos);
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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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///load read
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ha_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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}
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destory_R_buffer_block(&curr_sub_block);
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free(arg);
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return NULL;
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}
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void Counting_multiple_thr()
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{
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double start_time = Get_T();
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fprintf(stderr, "Begin Counting... \n");
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init_Total_Count_Table(asm_opt.k_mer_length, &TCB);
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pthread_t inputReadsHandle;
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int *is_insert = (int*)malloc(sizeof(*is_insert));
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*is_insert = 1;
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if (asm_opt.roundID == 0)
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{
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init_gz_files(&asm_opt);
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init_All_reads(&R_INF);
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init_R_buffer(asm_opt.thread_num);
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pthread_create(&inputReadsHandle, NULL, input_reads_muti_threads, (void*)is_insert);
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}
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pthread_t *_r_threads;
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_r_threads = (pthread_t *)malloc(sizeof(pthread_t)*asm_opt.thread_num);
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int i = 0;
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for (i = 0; i < asm_opt.thread_num; i++)
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{
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int *arg = (int*)malloc(sizeof(*arg));
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*arg = i;
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if (asm_opt.roundID == 0)
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{
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pthread_create(_r_threads + i, NULL, Perform_Counting, (void*)arg);
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}
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else
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{
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pthread_create(_r_threads + i, NULL, Perform_Counting_non_first, (void*)arg);
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}
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}
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for (i = 0; i < asm_opt.thread_num; i++)
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pthread_join(_r_threads[i], NULL);
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free(_r_threads);
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///destory_R_buffer();
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///destory_Total_Count_Table(&TCB);
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if (asm_opt.roundID == 0)
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{
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pthread_join(inputReadsHandle, NULL);
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///destory_kseq();
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destory_gz_files();
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}
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fprintf(stderr, "Counting has been completed.\n");
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fprintf(stderr, "%-30s%18.2f\n\n", "Counting time:", Get_T() - start_time);
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free(is_insert);
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}
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void Build_hash_table_multiple_thr()
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{
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double start_time = Get_T();
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fprintf(stderr, "Begin building hash table... \n");
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init_Total_Pos_Table(&PCB, &TCB);
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double T_start_time = Get_T();
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Traverse_Counting_Table(&TCB, &PCB, asm_opt.k_mer_min_freq, asm_opt.k_mer_max_freq);
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fprintf(stderr, "%-30s%18.2f\n\n", "Traverse time:", Get_T() - T_start_time);
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///at this moment, TCB can be free
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destory_Total_Count_Table(&TCB);
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pthread_t inputReadsHandle;
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int *is_insert = (int*)malloc(sizeof(*is_insert));
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*is_insert = 0;
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if (asm_opt.roundID == 0)
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{
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init_gz_files(&asm_opt);
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clear_R_buffer();
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malloc_All_reads(&R_INF);
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pthread_create(&inputReadsHandle, NULL, input_reads_muti_threads, (void*)is_insert);
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}
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pthread_t *_r_threads;
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_r_threads = (pthread_t *)malloc(sizeof(pthread_t) * asm_opt.thread_num);
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int i = 0;
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for (i = 0; i < asm_opt.thread_num; i++)
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{
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int *arg = (int*)malloc(sizeof(*arg));
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*arg = i;
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if (asm_opt.roundID == 0)
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{
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pthread_create(_r_threads + i, NULL, Build_hash_table, (void*)arg);
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}
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else
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{
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pthread_create(_r_threads + i, NULL, Build_hash_table_non_first, (void*)arg);
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}
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}
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if (asm_opt.roundID == 0)
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{
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pthread_join(inputReadsHandle, NULL);
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}
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for (i = 0; i < asm_opt.thread_num; i++)
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pthread_join(_r_threads[i], NULL);
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free(_r_threads);
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fprintf(stderr, "Hash table has been built.\n");
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fprintf(stderr, "%-30s%18.2f\n\n", "Build hash table time:", Get_T() - start_time);
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if (asm_opt.roundID == 0)
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{
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///destory_kseq();
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destory_gz_files();
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destory_R_buffer();
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}
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free(is_insert);
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}
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void get_corrected_read_from_cigar(Cigar_record* cigar, char* pre_read, int pre_length,
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char* new_read, int* new_length)
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void get_corrected_read_from_cigar(Cigar_record* cigar, char* pre_read, int pre_length, char* new_read, int* new_length)
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{
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int i, j;
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int pre_i, new_i;
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@@ -452,7 +39,7 @@ char* new_read, int* new_length)
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}
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else if (operation == 1)
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{
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for (j = 0; j < operation_length; j++)
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{
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new_read[new_i] = Get_MisMatch_Base(cigar->lost_base[diff_char_i]);
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@@ -499,7 +86,7 @@ void get_uncorrected_read_from_cigar(Cigar_record* cigar, char* new_read, int ne
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}
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else if (operation == 1)
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{
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for (j = 0; j < operation_length; j++)
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{
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pre_read[pre_i] = Get_Match_Base(cigar->lost_base[diff_char_i]);
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@@ -538,8 +125,7 @@ inline int get_cigar_errors(Cigar_record* cigar)
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return total_errors;
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}
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int debug_cigar(Cigar_record* cigar, char* pre_read, int pre_length,
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char* new_read, int new_length, int correct_base)
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int debug_cigar(Cigar_record* cigar, char* pre_read, int pre_length, char* new_read, int new_length, int correct_base)
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{
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int i;
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int total_errors = 0;
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@@ -556,13 +142,10 @@ char* new_read, int new_length, int correct_base)
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fprintf(stderr, "total_errors: %d, correct_base: %d\n", total_errors, correct_base);
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}
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int pre_i, new_i;
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int operation, operation_length;
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pre_i = new_i = 0;
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for (i = 0; i < (long long)cigar->length; i++)
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{
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operation = Get_Cigar_Type(cigar->record[i]);
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@@ -589,24 +172,21 @@ char* new_read, int new_length, int correct_base)
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{
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new_i = new_i + operation_length;
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}
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}
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if (pre_i != pre_length)
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{
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fprintf(stderr, "pre_i: %d, pre_length: %d\n", pre_i, pre_length);
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}
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if(new_i != new_length)
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{
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fprintf(stderr, "new_i: %d, new_length: %d\n", new_i, new_length);
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}
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return 1;
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char* tmp_seq = (char*)malloc(new_length + pre_length);
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int tmp_length;
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@@ -624,12 +204,9 @@ char* new_read, int new_length, int correct_base)
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}
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get_uncorrected_read_from_cigar(cigar, new_read, new_length, tmp_seq, &tmp_length);
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if(tmp_length != pre_length)
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{
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fprintf(stderr, "tmp_length: %d, pre_length: %d\n", tmp_length, pre_length);
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@@ -639,7 +216,7 @@ char* new_read, int new_length, int correct_base)
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{
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fprintf(stderr, "error pre string\n");
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}
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||||
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free(tmp_seq);
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@@ -652,7 +229,6 @@ char* new_read, int new_length, int correct_base)
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||||
|
||||
inline void push_cigar(Compressed_Cigar_record* records, long long ID, Cigar_record* input)
|
||||
{
|
||||
|
||||
if (input->length > records[ID].size)
|
||||
{
|
||||
records[ID].size = input->length;
|
||||
@@ -673,8 +249,7 @@ inline void push_cigar(Compressed_Cigar_record* records, long long ID, Cigar_rec
|
||||
}
|
||||
|
||||
|
||||
void push_overlaps(ma_hit_t_alloc* paf, overlap_region_alloc* overlap_list, int flag,
|
||||
All_reads* R_INF, int if_reverse)
|
||||
void push_overlaps(ma_hit_t_alloc* paf, overlap_region_alloc* overlap_list, int flag, All_reads* R_INF, int if_reverse)
|
||||
{
|
||||
long long i = 0, xLen, yLen;
|
||||
ma_hit_t tmp;
|
||||
@@ -689,7 +264,7 @@ All_reads* R_INF, int if_reverse)
|
||||
tmp.qns = overlap_list->list[i].x_id;
|
||||
tmp.qns = tmp.qns << 32;
|
||||
tmp.tn = overlap_list->list[i].y_id;
|
||||
|
||||
|
||||
if(if_reverse != 0)
|
||||
{
|
||||
tmp.qns = tmp.qns | (uint64_t)(xLen - overlap_list->list[i].x_pos_s - 1);
|
||||
@@ -704,8 +279,8 @@ All_reads* R_INF, int if_reverse)
|
||||
tmp.ts = overlap_list->list[i].y_pos_s;
|
||||
tmp.te = overlap_list->list[i].y_pos_e;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
///for overlap_list, the x_strand of all overlaps are 0, so the tmp.rev is the same as the y_strand
|
||||
tmp.rev = overlap_list->list[i].y_pos_strand;
|
||||
|
||||
@@ -717,12 +292,9 @@ All_reads* R_INF, int if_reverse)
|
||||
add_ma_hit_t_alloc(paf, &tmp);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
int if_exact_match(char* x, long long xLen, char* y, long long yLen,
|
||||
long long xBeg, long long xEnd, long long yBeg, long long yEnd)
|
||||
int if_exact_match(char* x, long long xLen, char* y, long long yLen, long long xBeg, long long xEnd, long long yBeg, long long yEnd)
|
||||
{
|
||||
long long overlapLen = xEnd - xBeg + 1;
|
||||
|
||||
@@ -743,12 +315,11 @@ long long xBeg, long long xEnd, long long yBeg, long long yEnd)
|
||||
return 1;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
long long push_final_overlaps(ma_hit_t_alloc* paf, ma_hit_t_alloc* reverse_paf_list,
|
||||
overlap_region_alloc* overlap_list, int flag)
|
||||
long long push_final_overlaps(ma_hit_t_alloc* paf, ma_hit_t_alloc* reverse_paf_list, overlap_region_alloc* overlap_list, int flag)
|
||||
{
|
||||
long long i = 0;
|
||||
long long available_overlaps = 0;
|
||||
@@ -790,7 +361,7 @@ overlap_region_alloc* overlap_list, int flag)
|
||||
///the end pos is open
|
||||
tmp.te++;
|
||||
/**********************target***************************/
|
||||
|
||||
|
||||
tmp.bl = R_INF.read_length[overlap_list->list[i].y_id];
|
||||
tmp.ml = overlap_list->list[i].strong;
|
||||
tmp.no_l_indel = overlap_list->list[i].without_large_indel;
|
||||
@@ -835,7 +406,7 @@ void get_new_candidates(long long readID, UC_Read* g_read, overlap_region_alloc*
|
||||
avalible_k++;
|
||||
if (avalible_k >= asm_opt.k_mer_length)
|
||||
{
|
||||
list_length = locate_Total_Pos_Table(&PCB, &k_code, &list, asm_opt.k_mer_length, &sub_ID);
|
||||
//list_length = locate_Total_Pos_Table(&PCB, &k_code, &list, asm_opt.k_mer_length, &sub_ID);
|
||||
|
||||
if (list_length != 0)
|
||||
{
|
||||
@@ -950,7 +521,7 @@ void* Overlap_calculate_heap_merge(void* arg)
|
||||
destory_Correct_dumy(&correct);
|
||||
destoryHaplotypeEvdience(&hap);
|
||||
destory_Round2_alignment(&second_round);
|
||||
|
||||
|
||||
|
||||
|
||||
pthread_mutex_lock(&statistics);
|
||||
@@ -988,7 +559,7 @@ void* Output_related_reads(void* arg)
|
||||
init_Graph(&DAGCon);
|
||||
init_Graph(&POA_Graph);
|
||||
|
||||
|
||||
|
||||
init_Candidates_list(&l);
|
||||
//init_Candidates_list(&debug_l);
|
||||
|
||||
@@ -1021,7 +592,7 @@ void* Output_related_reads(void* arg)
|
||||
long long required_read_name_length = strlen(asm_opt.required_read_name);
|
||||
for (i = thr_ID; i < (long long)R_INF.total_reads; i = i + asm_opt.thread_num)
|
||||
{
|
||||
|
||||
|
||||
if(required_read_name_length == (long long)Get_NAME_LENGTH((R_INF),i)
|
||||
&&
|
||||
memcmp(asm_opt.required_read_name, Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0)
|
||||
@@ -1043,7 +614,7 @@ void* Output_related_reads(void* arg)
|
||||
recover_UC_Read(&g_read, &R_INF, overlap_list.list[k].y_id);
|
||||
fprintf(stderr, "%.*s\n", (int)g_read.length, g_read.seq);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
@@ -1061,7 +632,7 @@ void* Output_related_reads(void* arg)
|
||||
destory_Correct_dumy(&correct);
|
||||
destoryHaplotypeEvdience(&hap);
|
||||
destory_Round2_alignment(&second_round);
|
||||
|
||||
|
||||
|
||||
free(arg);
|
||||
|
||||
@@ -1103,7 +674,7 @@ void* Save_corrected_reads(void* arg)
|
||||
|
||||
char* new_read;
|
||||
int new_read_length;
|
||||
|
||||
|
||||
for (i = thr_ID; i < (long long)R_INF.total_reads; i = i + asm_opt.thread_num)
|
||||
{
|
||||
recover_UC_Read(&g_read, &R_INF, i);
|
||||
@@ -1121,7 +692,7 @@ void* Save_corrected_reads(void* arg)
|
||||
cigar.lost_base = R_INF.cigars[i].lost_base;
|
||||
|
||||
get_corrected_read_from_cigar(&cigar, g_read.seq, g_read.length, first_round_read, &first_round_read_length);
|
||||
|
||||
|
||||
/********************************1 round******************************/
|
||||
|
||||
/********************************2 round******************************/
|
||||
@@ -1136,16 +707,16 @@ void* Save_corrected_reads(void* arg)
|
||||
cigar.lost_base = R_INF.second_round_cigar[i].lost_base;
|
||||
get_corrected_read_from_cigar(&cigar, first_round_read, first_round_read_length,
|
||||
second_round_read, &second_round_read_length);
|
||||
|
||||
|
||||
/********************************2 round******************************/
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
new_read = second_round_read;
|
||||
new_read_length = second_round_read_length;
|
||||
|
||||
|
||||
|
||||
if (asm_opt.roundID != asm_opt.number_of_round - 1)
|
||||
{
|
||||
///need modification
|
||||
@@ -1157,10 +728,10 @@ void* Save_corrected_reads(void* arg)
|
||||
reverse_complement(new_read, new_read_length);
|
||||
}
|
||||
|
||||
|
||||
|
||||
N_occ = get_N_occ(new_read, new_read_length);
|
||||
|
||||
|
||||
|
||||
if((long long)R_INF.read_size[i] < new_read_length)
|
||||
{
|
||||
R_INF.read_size[i] = new_read_length;
|
||||
@@ -1168,7 +739,7 @@ void* Save_corrected_reads(void* arg)
|
||||
}
|
||||
|
||||
R_INF.read_length[i] = new_read_length;
|
||||
|
||||
|
||||
|
||||
ha_compress_base(Get_READ(R_INF, i),
|
||||
new_read, new_read_length,
|
||||
@@ -1210,9 +781,9 @@ void Output_corrected_reads()
|
||||
void Overlap_calculate_multipe_thr()
|
||||
{
|
||||
double start_time = Get_T();
|
||||
|
||||
|
||||
fprintf(stderr, "Begin calculating overlaps... \n");
|
||||
|
||||
|
||||
pthread_t *_r_threads;
|
||||
|
||||
_r_threads = (pthread_t *)malloc(sizeof(pthread_t)*asm_opt.thread_num);
|
||||
@@ -1232,7 +803,7 @@ void Overlap_calculate_multipe_thr()
|
||||
pthread_create(_r_threads + i, NULL, Output_related_reads, (void*)arg);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
for (i = 0; i < asm_opt.thread_num; i++)
|
||||
pthread_join(_r_threads[i], NULL);
|
||||
@@ -1246,7 +817,8 @@ void Overlap_calculate_multipe_thr()
|
||||
}
|
||||
|
||||
|
||||
destory_Total_Pos_Table(&PCB);
|
||||
ha_idx_destroy(ha_idx);
|
||||
ha_idx = 0;
|
||||
|
||||
fprintf(stderr, "All overlaps have been calculated.\n");
|
||||
|
||||
@@ -1269,14 +841,14 @@ void Overlap_calculate_multipe_thr()
|
||||
|
||||
fprintf(stderr, "%-30s%18.2f\n\n", "Corrected read saving time:", Get_T() - start_time);
|
||||
|
||||
|
||||
|
||||
///only the last round can output read to disk
|
||||
if (asm_opt.roundID == asm_opt.number_of_round - 1)
|
||||
{
|
||||
start_time = Get_T();
|
||||
|
||||
|
||||
Output_corrected_reads();
|
||||
|
||||
|
||||
fprintf(stderr, "%-30s%18.2f\n\n", "Output time:", Get_T() - start_time);
|
||||
}
|
||||
}
|
||||
@@ -1357,7 +929,7 @@ UC_Read* g_read, UC_Read* overlap_read, int is_match, int is_exact)
|
||||
{
|
||||
overlap_list->list[j].is_match = 3;
|
||||
}
|
||||
|
||||
|
||||
j++;
|
||||
inner_j++;
|
||||
}
|
||||
@@ -1400,7 +972,7 @@ void statistic(ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, long long readNum)
|
||||
long long forward, reverse, strong, weak, exact, no_l_indel;
|
||||
no_l_indel = forward = reverse = exact = strong = weak = 0;
|
||||
long long i, j;
|
||||
|
||||
|
||||
for (i = 0; i < readNum; i++)
|
||||
{
|
||||
forward += paf[i].length;
|
||||
@@ -1495,7 +1067,7 @@ long long x_readLen, long long y_readLen, Cigar_record* cigar, uint8_t* c2n)
|
||||
// if(bandLen == 0) bandLen = MIN(xRegionLen, yRegionLen);
|
||||
}
|
||||
|
||||
|
||||
|
||||
///do alignment forward
|
||||
kv_resize(uint8_t, x_num, (uint64_t)xRegionLen);
|
||||
kv_resize(uint8_t, y_num, (uint64_t)yRegionLen);
|
||||
@@ -1519,9 +1091,9 @@ UC_Read* g_read, UC_Read* overlap_read, uint8_t* c2n)
|
||||
char* y_string;
|
||||
Cigar_record* cigar;
|
||||
resize_Cigar_record_alloc(cigarline, overlap_list->length);
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
for (i = 0; i < overlap_list->length; i++)
|
||||
{
|
||||
if(overlap_list->list[i].is_match == 1 ||
|
||||
@@ -1554,10 +1126,10 @@ UC_Read* g_read, UC_Read* overlap_read, uint8_t* c2n)
|
||||
Get_READ_LENGTH(R_INF, overlap_list->list[i].x_id),
|
||||
Get_READ_LENGTH(R_INF, overlap_list->list[i].y_id), cigar, c2n);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
void* Final_overlap_calculate_heap_merge(void* arg)
|
||||
@@ -1617,7 +1189,7 @@ void* Final_overlap_calculate_heap_merge(void* arg)
|
||||
push_final_overlaps(&(R_INF.reverse_paf[i]), R_INF.reverse_paf,
|
||||
&overlap_list, 2);
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
finish_output_buffer();
|
||||
@@ -1628,7 +1200,7 @@ void* Final_overlap_calculate_heap_merge(void* arg)
|
||||
destory_UC_Read(&g_read);
|
||||
destory_UC_Read(&overlap_read);
|
||||
destory_Cigar_record_alloc(&cigarline);
|
||||
|
||||
|
||||
|
||||
pthread_mutex_lock(&statistics);
|
||||
asm_opt.complete_threads++;
|
||||
@@ -1685,7 +1257,7 @@ void Output_PAF()
|
||||
fprintf(output_file, "%d\t", sources[i].buffer[j].ml);
|
||||
fprintf(output_file, "%d\t", sources[i].buffer[j].bl);
|
||||
fprintf(output_file, "255\n");
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
@@ -1712,7 +1284,7 @@ int check_cluster(uint64_t* list, long long listLen, ma_hit_t_alloc* paf, float
|
||||
{
|
||||
A_edges++;
|
||||
}
|
||||
|
||||
|
||||
if(get_specific_overlap(&(paf[tn]), tn, qn) != -1)
|
||||
{
|
||||
A_edges++;
|
||||
@@ -1720,7 +1292,7 @@ int check_cluster(uint64_t* list, long long listLen, ma_hit_t_alloc* paf, float
|
||||
|
||||
T_edges = T_edges + 2;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
if(A_edges >= (T_edges*threshold))
|
||||
@@ -1747,7 +1319,7 @@ long long readNum, long long rescue_threshold, float cluster_threshold)
|
||||
kv_init(edge_vector_index);
|
||||
uint64_t flag;
|
||||
int index;
|
||||
|
||||
|
||||
for (i = 0; i < readNum; i++)
|
||||
{
|
||||
edge_vector.n = 0;
|
||||
@@ -1813,15 +1385,13 @@ long long readNum, long long rescue_threshold, float cluster_threshold)
|
||||
}
|
||||
|
||||
|
||||
|
||||
void generate_overlaps(int last_round)
|
||||
{
|
||||
double start_time = Get_T();
|
||||
asm_opt.roundID = asm_opt.number_of_round - last_round;
|
||||
fprintf(stderr, "Begin calculting final overlaps ...\n");
|
||||
|
||||
Counting_multiple_thr();
|
||||
Build_hash_table_multiple_thr();
|
||||
ha_idx = ha_gen_mzidx(&asm_opt, ha_flt_tab, asm_opt.roundID == 0? 0 : 1, &R_INF);
|
||||
|
||||
pthread_t *_r_threads;
|
||||
|
||||
@@ -1835,14 +1405,15 @@ void generate_overlaps(int last_round)
|
||||
*arg = i;
|
||||
pthread_create(_r_threads + i, NULL, Final_overlap_calculate_heap_merge, (void*)arg);
|
||||
}
|
||||
|
||||
|
||||
|
||||
for (i = 0; i < asm_opt.thread_num; i++)
|
||||
pthread_join(_r_threads[i], NULL);
|
||||
free(_r_threads);
|
||||
|
||||
///rescue_edges(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads, 4, 0.985);
|
||||
destory_Total_Pos_Table(&PCB);
|
||||
ha_idx_destroy(ha_idx);
|
||||
ha_idx = 0;
|
||||
|
||||
fprintf(stderr, "Final overlaps have been calculated.\n");
|
||||
fprintf(stderr, "%-30s%18.2f\n\n", "Final overlaps calculation time:", Get_T() - start_time);
|
||||
@@ -1850,7 +1421,7 @@ void generate_overlaps(int last_round)
|
||||
Output_PAF();
|
||||
|
||||
trio_partition();
|
||||
|
||||
|
||||
build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf,
|
||||
R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round,
|
||||
asm_opt.gap_fuzz, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name,
|
||||
@@ -1860,20 +1431,18 @@ void generate_overlaps(int last_round)
|
||||
|
||||
void Correct_Reads(int last_round)
|
||||
{
|
||||
|
||||
if(asm_opt.load_index_from_disk && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf,
|
||||
asm_opt.output_file_name))
|
||||
if (asm_opt.load_index_from_disk && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf, asm_opt.output_file_name))
|
||||
{
|
||||
build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf,
|
||||
R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round,
|
||||
asm_opt.gap_fuzz, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name, asm_opt.large_pop_bubble_size, 0, 0);
|
||||
exit(1);
|
||||
exit(0);
|
||||
}
|
||||
else
|
||||
{
|
||||
///fprintf(stderr, "Cannot find overlap file. Please run the whole hifiasm.\n");
|
||||
}
|
||||
|
||||
|
||||
clear_opt(&asm_opt, last_round);
|
||||
|
||||
if(last_round == 0)
|
||||
@@ -1881,12 +1450,12 @@ void Correct_Reads(int last_round)
|
||||
generate_overlaps(last_round);
|
||||
return;
|
||||
}
|
||||
|
||||
|
||||
fprintf(stderr, "Error correction: Start the %d-th round ...\n", asm_opt.roundID);
|
||||
|
||||
Counting_multiple_thr();
|
||||
Build_hash_table_multiple_thr();
|
||||
|
||||
ha_idx = ha_gen_mzidx(&asm_opt, ha_flt_tab, asm_opt.roundID == 0? 0 : 1, &R_INF);
|
||||
Overlap_calculate_multipe_thr();
|
||||
ha_idx_destroy(ha_idx);
|
||||
|
||||
fprintf(stderr, "Error correction: The %d-th round has been completed.\n", asm_opt.roundID);
|
||||
|
||||
|
||||
Reference in New Issue
Block a user