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Finish multiple thread counting

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This commit is contained in:
Haoyu Cheng
2019-05-12 02:16:20 -04:00
parent 94bd75e576
commit 9302fc6058
25 changed files with 1209 additions and 34 deletions
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143
Assembly.cpp
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@@ -4,11 +4,15 @@
#include <zlib.h>
#include "Process_Read.h"
#include "CommandLines.h"
#include "kmer.h"
#include "Hash_Table.h"
Total_Count_Table TCB;
void Counting()
/********************************for debug***************************************/
void Verify_Counting()
{
@@ -17,46 +21,87 @@ void Counting()
long long read_number = 0;
HPC_seq HPC_read;
uint64_t code;
Hash_code k_code;
int avalible_k = 0;
fprintf(stdout, "Start Verifying ...\n");
while (get_read(seq))
{
fprintf(stderr,"@%s\n",seq->name.s);
fprintf(stderr,"%s\n",seq->seq.s);
fprintf(stderr,"+\n");
fprintf(stderr,"%s\n",seq->qual.s);
init_HPC_seq(&HPC_read, seq->seq.s, seq->seq.l);
init_Hash_code(&k_code);
avalible_k = 0;
while ((code = get_HPC_code(&HPC_read)) != 6)
{
if(code < 4)
{
k_mer_append(&k_code,code,k_mer_length);
avalible_k++;
if (avalible_k>=k_mer_length)
{
if(verify_Total_Count_Table(&TCB, &k_code, k_mer_length) == -1)
{
fprintf(stderr, "ERROR when subtracting!\n");
}
}
}
else
{
avalible_k = 0;
init_Hash_code(&k_code);
}
}
read_number++;
}
fprintf(stdout, "read_number: %lld\n",read_number);
fprintf(stdout, "Start Traversing ...\n");
Traverse_Total_Count_Table(&TCB);
fprintf(stdout, "Finish Traversing!\n");
}
/********************************for debug***************************************/
void* Perform_Counting(void* arg)
{
int thr_ID = *((int*)arg);
int i = 0;
HPC_seq HPC_read;
R_buffer_block curr_sub_block;
init_R_buffer_block(&curr_sub_block);
long long read_number = 0;
long long k_mer_number = 0 ;
int file_flag = 1;
uint64_t code;
Hash_code k_code;
int avalible_k = 0;
while (file_flag != 0)
{
@@ -64,10 +109,46 @@ void* Perform_Counting(void* arg)
read_number = read_number + curr_sub_block.num;
for (i = 0; i < curr_sub_block.num; i++)
{
init_HPC_seq(&HPC_read, curr_sub_block.read[i].seq.s, curr_sub_block.read[i].seq.l);
init_Hash_code(&k_code);
avalible_k = 0;
while ((code = get_HPC_code(&HPC_read)) != 6)
{
if(code < 4)
{
k_mer_append(&k_code,code,k_mer_length);
avalible_k++;
if (avalible_k>=k_mer_length)
{
///插入
insert_Total_Count_Table(&TCB, &k_code, k_mer_length);
k_mer_number++;
}
}
else
{
avalible_k = 0;
init_Hash_code(&k_code);
}
}
}
}
fprintf(stdout, "#########read_number: %lld\n",read_number);
fflush(stdout);
destory_R_buffer_block(&curr_sub_block);
free(arg);
fprintf(stdout, "thr_ID: %d, read_number: %lld, k_mer_number: %lld\n",thr_ID, read_number, k_mer_number);
}
@@ -89,6 +170,15 @@ void* Perform_Counting(void* arg)
void Counting_multiple_thr()
{
init_Total_Count_Table(k_mer_length, &TCB);
fprintf(stdout, "TCB.prefix_bits: %d\n", TCB.prefix_bits);
fprintf(stdout, "TCB.suffix_bits: %d\n", TCB.suffix_bits);
fprintf(stdout, "TCB.size: %d\n", TCB.size);
pthread_t inputReadsHandle;
init_R_buffer(thread_num);
@@ -120,6 +210,11 @@ void Counting_multiple_thr()
free(_r_threads);
destory_R_buffer();
destory_Total_Count_Table(&TCB);
}
@@ -134,6 +229,14 @@ void Counting_multiple_thr()