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Process_sam_out.cpp
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Process_sam_out.cpp
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/*
Authors:
Haoyu Cheng
chhy@mail.ustc.edu.cn
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "Auxiliary.h"
#include "Process_sam_out.h"
#include <pthread.h>
pthread_mutex_t o_readinputMutex;
pthread_mutex_t o_queueMutex;
pthread_mutex_t o_terminateMutex;
pthread_cond_t o_flushCond;
pthread_cond_t o_readinputflushCond;
pthread_cond_t o_stallCond;
pthread_cond_t o_readinputstallCond;
pthread_mutex_t o_doneMutex;
FILE *_out_fp;
FILE *_out_fp_methy1;
FILE *_out_fp_methy2;
FILE *_out_fp_methy3;
int sub_block_init_length = 10000;
Output_buffer buffer_out;
Output_buffer_sub_block tmp_buffer_sub_block;
Output_methy_buffer buffer_methy_out;
Methylation tmp_methy_sub_block;
Pair_Methylation tmp_methy_sub_block_PE;
Output_methy_buffer_pair buffer_methy_out_PE;
void output_single_methy_CpG
(bitmapper_bs_iter tmp_pos, char* chrome_name, int nmethyl, int total)
{
int nunmethyl = total - nmethyl;
double precent;
if (total == 0)
{
precent = 0;
}
else
{
precent = (double)nmethyl / (double)total;
}
fprintf(_out_fp_methy1, "%s\t%llu\t%llu\t%d\t%d\t%d\n",
chrome_name, tmp_pos, tmp_pos + 1, (int)(precent * 100), nmethyl, nunmethyl);
}
void output_methy_directly(Output_buffer_sub_block* CpG_buffer, Output_buffer_sub_block* CHG_buffer, Output_buffer_sub_block* CHH_buffer)
{
if (CpG)
{
/**
CpG_buffer->buffer[CpG_buffer->length] = '\0';
fprintf(_out_fp_methy1, "%s", CpG_buffer->buffer);
**/
fwrite(CpG_buffer->buffer, 1, CpG_buffer->length, _out_fp_methy1);
CpG_buffer->length = 0;
}
if (CHG)
{
/**
CHG_buffer->buffer[CHG_buffer->length] = '\0';
fprintf(_out_fp_methy2, "%s", CHG_buffer->buffer);
**/
fwrite(CHG_buffer->buffer, 1, CHG_buffer->length, _out_fp_methy2);
CHG_buffer->length = 0;
}
if (CHH)
{
/**
CHH_buffer->buffer[CHH_buffer->length] = '\0';
fprintf(_out_fp_methy3, "%s", CHH_buffer->buffer);
**/
fwrite(CHH_buffer->buffer, 1, CHH_buffer->length, _out_fp_methy3);
CHH_buffer->length = 0;
}
}
void output_single_methy_multiple_thread
(bitmapper_bs_iter tmp_pos, char* chrome_name, int nmethyl, int total, Output_buffer_sub_block* buffer)
{
int nunmethyl = total - nmethyl;
double precent;
if (total == 0)
{
precent = 0;
}
else
{
precent = (double)nmethyl / (double)total;
}
/**
fprintf(_out_fp_methy1, "%s\t%llu\t%llu\t%d\t%d\t%d\n",
chrome_name, tmp_pos, tmp_pos + 1, (int)(precent * 100), nmethyl, nunmethyl);
**/
output_to_buffer_char_no_length(buffer, chrome_name);
//��������ʱ��32����������������\t����Ҫ�����
buffer->buffer[buffer->length] = '\t';
buffer->length++;
output_to_buffer_int(buffer, tmp_pos);
//��������ʱ��32����������������\t����Ҫ�����
buffer->buffer[buffer->length] = '\t';
buffer->length++;
output_to_buffer_int(buffer, tmp_pos + 1);
//��������ʱ��32����������������\t����Ҫ�����
buffer->buffer[buffer->length] = '\t';
buffer->length++;
output_to_buffer_int(buffer, (int)(precent * 100));
//��������ʱ��32����������������\t����Ҫ�����
buffer->buffer[buffer->length] = '\t';
buffer->length++;
output_to_buffer_int(buffer, nmethyl);
//��������ʱ��32����������������\t����Ҫ�����
buffer->buffer[buffer->length] = '\t';
buffer->length++;
output_to_buffer_int(buffer, nunmethyl);
//��������ʱ��32����������������\t����Ҫ�����
buffer->buffer[buffer->length] = '\n';
buffer->length++;
}
void output_single_methy_CHG
(bitmapper_bs_iter tmp_pos,
char* chrome_name,
int nmethyl,
int total)
{
int nunmethyl = total - nmethyl;
double precent;
if (total == 0)
{
precent = 0;
}
else
{
precent = (double)nmethyl / (double)total;
}
fprintf(_out_fp_methy2, "%s\t%llu\t%llu\t%d\t%d\t%d\n",
chrome_name, tmp_pos, tmp_pos + 1, (int)(precent * 100), nmethyl, nunmethyl);
}
void output_single_methy_CHH
(bitmapper_bs_iter tmp_pos,
char* chrome_name,
int nmethyl,
int total)
{
int nunmethyl = total - nmethyl;
double precent;
if (total == 0)
{
precent = 0;
}
else
{
precent = (double)nmethyl / (double)total;
}
fprintf(_out_fp_methy3, "%s\t%llu\t%llu\t%d\t%d\t%d\n",
chrome_name, tmp_pos, tmp_pos + 1, (int)(precent * 100), nmethyl, nunmethyl);
}
int init_output_methy(char *fileName, int* need_context)
{
char output_name[NAME_LENGTH];
if (need_context[0])
{
sprintf(output_name, "%s_CpG.bedGraph", fileName);
fprintf(stderr, "Output CpG context methylation metrics to %s ...\n", output_name);
_out_fp_methy1 = fopen(output_name, "w");
if (_out_fp_methy1 == NULL)
{
return 0;
}
fprintf(_out_fp_methy1, "track type=\"bedGraph\" description=\"CpG methylation levels\"\n");
}
if (need_context[1])
{
sprintf(output_name, "%s_CHG.bedGraph", fileName);
fprintf(stderr, "Output CHG context methylation metrics to %s ...\n", output_name);
_out_fp_methy2 = fopen(output_name, "w");
if (_out_fp_methy2 == NULL)
{
return 0;
}
fprintf(_out_fp_methy2, "track type=\"bedGraph\" description=\"CHG methylation levels\"\n");
}
if (need_context[2])
{
sprintf(output_name, "%s_CHH.bedGraph", fileName);
fprintf(stderr, "Output CHH context methylation metrics to %s ...\n", output_name);
_out_fp_methy3 = fopen(output_name, "w");
if (_out_fp_methy3 == NULL)
{
return 0;
}
fprintf(_out_fp_methy3, "track type=\"bedGraph\" description=\"CHH methylation levels\"\n");
}
return 1;
}
///void finalizeTXOutput()
void finalizeOutput()
{
fclose(_out_fp);
}
void init_buffer_sub_block(Output_buffer_sub_block* sub_block)
{
sub_block->length = 0;
sub_block->size = sub_block_init_length;
sub_block->buffer = (char*)malloc(sub_block->size);
}
///��ʼ��������
void init_output_buffer(int thread_number)
{
///ouput_buffer_size
///size�ǿռ��С
buffer_out.sub_block_size = ouput_buffer_size * thread_number;
buffer_out.sub_block_number = 0;
buffer_out.sub_buffer = (Output_buffer_sub_block*)malloc(sizeof(Output_buffer_sub_block)*buffer_out.sub_block_size);
for (int i = 0; i < buffer_out.sub_block_size; i++)
{
init_buffer_sub_block(&(buffer_out.sub_buffer[i]));
}
buffer_out.all_buffer_end = 0;
}
void init_output_methy_buffer(int thread_number)
{
///ouput_buffer_size
///size�ǿռ��С
buffer_methy_out.sub_block_size = methylation_buffer_times * thread_number;
buffer_methy_out.sub_block_number = 0;
buffer_methy_out.sub_buffer =
(Methylation*)malloc(sizeof(Methylation)*buffer_methy_out.sub_block_size);
for (int i = 0; i < buffer_methy_out.sub_block_size; i++)
{
init_methylation(&(buffer_methy_out.sub_buffer[i]), methylation_size);
}
buffer_methy_out.all_buffer_end = 0;
}
void init_output_methy_buffer_pair(int thread_number)
{
///ouput_buffer_size
///size�ǿռ��С
buffer_methy_out_PE.sub_block_size = methylation_buffer_times * thread_number;
buffer_methy_out_PE.sub_block_number = 0;
buffer_methy_out_PE.sub_buffer =
(Pair_Methylation*)malloc(sizeof(Pair_Methylation)*buffer_methy_out_PE.sub_block_size);
for (int i = 0; i < buffer_methy_out_PE.sub_block_size; i++)
{
///ע������Ҫ����2
init_pair_methylation(&(buffer_methy_out_PE.sub_buffer[i]), methylation_size/2);
}
buffer_methy_out_PE.all_buffer_end = 0;
}
inline int if_empty_buffer()
{
if (buffer_out.sub_block_number == 0)
{
return 1;
}
else
{
return 0;
}
}
inline int if_empty_methy_buffer()
{
if (buffer_methy_out.sub_block_number == 0)
{
return 1;
}
else
{
return 0;
}
}
inline int if_empty_methy_buffer_pair()
{
if (buffer_methy_out_PE.sub_block_number == 0)
{
return 1;
}
else
{
return 0;
}
}
inline int if_full_buffer()
{
if (buffer_out.sub_block_number >= buffer_out.sub_block_size)
{
return 1;
}
else
{
return 0;
}
}
inline int if_full_methy_buffer()
{
if (buffer_methy_out.sub_block_number >= buffer_methy_out.sub_block_size)
{
return 1;
}
else
{
return 0;
}
}
inline int if_full_methy_buffer_pair()
{
if (buffer_methy_out_PE.sub_block_number >= buffer_methy_out_PE.sub_block_size)
{
return 1;
}
else
{
return 0;
}
}
///�����Ҫȡһ�����ȡ��curr_sub_block��
inline void pop_single_buffer(Output_buffer_sub_block* curr_sub_block)
{
buffer_out.sub_block_number--;
///ֻ����ָ��
///�ǵ�Ҫ������ֱ�Ӹ�ֵ���ڴ�й¶�����Ұָ��
char *k;
k = buffer_out.sub_buffer[buffer_out.sub_block_number].buffer;
buffer_out.sub_buffer[buffer_out.sub_block_number].buffer = curr_sub_block->buffer;
curr_sub_block->buffer = k;
long long tmp_size;
tmp_size = curr_sub_block->size;
curr_sub_block->size = buffer_out.sub_buffer[buffer_out.sub_block_number].size;
buffer_out.sub_buffer[buffer_out.sub_block_number].size = tmp_size;
curr_sub_block->length = buffer_out.sub_buffer[buffer_out.sub_block_number].length;
buffer_out.sub_buffer[buffer_out.sub_block_number].length = 0;
}
///buffer_methy_out
inline void pop_single_methy_buffer(Methylation* curr_sub_block)
{
buffer_methy_out.sub_block_number--;
///����ռ�Ӧ����genome_cut+1
bitmapper_bs_iter* cut_index; ///���Ҫ����
///���ĸ����鹹��һ��������Ԫ��
bitmapper_bs_iter* sites; ///���Ҫ����
uint16_t* r_length; ///���Ҫ����
uint16_t* r_real_length; ///���Ҫ����
uint16_t* r_size_3_bit; ///���Ҫ����
bitmapper_bs_iter** reads_3_bit; ///���Ҫ����
cut_index = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].cut_index;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].cut_index = curr_sub_block->cut_index;
curr_sub_block->cut_index = cut_index;
sites = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].sites;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].sites = curr_sub_block->sites;
curr_sub_block->sites = sites;
r_length = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_length;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_length = curr_sub_block->r_length;
curr_sub_block->r_length = r_length;
/*************����Ҫ��**************/
/**
r_size = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_size;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_size = curr_sub_block->r_size;
curr_sub_block->r_size = r_size;
reads = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].reads;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].reads = curr_sub_block->reads;
curr_sub_block->reads = reads;
**/
r_size_3_bit = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_size_3_bit;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_size_3_bit = curr_sub_block->r_size_3_bit;
curr_sub_block->r_size_3_bit = r_size_3_bit;
reads_3_bit = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].reads_3_bit;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].reads_3_bit = curr_sub_block->reads_3_bit;
curr_sub_block->reads_3_bit = reads_3_bit;
r_real_length = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_real_length;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_real_length = curr_sub_block->r_real_length;
curr_sub_block->r_real_length = r_real_length;
/*************����Ҫ��**************/
curr_sub_block->current_size = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].current_size;
///���clearӦ���ǿ��Բ�Ҫ��
clear_methylation(&(buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number]));
}
inline void pop_single_methy_buffer_pair(Pair_Methylation* curr_sub_block)
{
buffer_methy_out_PE.sub_block_number--;
///����ռ�Ӧ����genome_cut+1
bitmapper_bs_iter* cut_index; ///���Ҫ����
Single_Methylation tmp_R;///���Ҫ����
cut_index = buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].cut_index;
buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].cut_index = curr_sub_block->cut_index;
curr_sub_block->cut_index = cut_index;
///��һ��read
tmp_R = buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].R[0];
buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].R[0] = curr_sub_block->R[0];
curr_sub_block->R[0] = tmp_R;
///�ڶ���read
tmp_R = buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].R[1];
buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].R[1] = curr_sub_block->R[1];
curr_sub_block->R[1] = tmp_R;
curr_sub_block->current_size = buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].current_size;
///���clearӦ���ǿ��Բ�Ҫ��
clear_methylation_pair(&(buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number]));
}
///�����Ҫ��curr_sub_block�Ľ���ŵ�������
inline void push_single_buffer(Output_buffer_sub_block* curr_sub_block)
{
///ֻ����ָ��
///�ǵ�Ҫ������ֱ�Ӹ�ֵ���ڴ�й¶�����Ұָ��
char *k;
k = buffer_out.sub_buffer[buffer_out.sub_block_number].buffer;
buffer_out.sub_buffer[buffer_out.sub_block_number].buffer = curr_sub_block->buffer;
curr_sub_block->buffer = k;
long long tmp_size;
tmp_size = curr_sub_block->size;
curr_sub_block->size = buffer_out.sub_buffer[buffer_out.sub_block_number].size;
buffer_out.sub_buffer[buffer_out.sub_block_number].size = tmp_size;
buffer_out.sub_buffer[buffer_out.sub_block_number].length = curr_sub_block->length;
curr_sub_block->length = 0;
buffer_out.sub_block_number++;
}
///�����Ҫ��curr_sub_block�Ľ���ŵ�������
inline void push_single_methy_buffer(Methylation* curr_sub_block)
{
///����ռ�Ӧ����genome_cut+1
bitmapper_bs_iter* cut_index; ///���Ҫ����
///���ĸ����鹹��һ��������Ԫ��
bitmapper_bs_iter* sites; ///���Ҫ����
uint16_t* r_length; ///���Ҫ����
uint16_t* r_real_length; ///���Ҫ����
uint16_t* r_size_3_bit; ///���Ҫ����
bitmapper_bs_iter** reads_3_bit; ///���Ҫ����
cut_index = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].cut_index;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].cut_index = curr_sub_block->cut_index;
curr_sub_block->cut_index = cut_index;
sites = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].sites;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].sites = curr_sub_block->sites;
curr_sub_block->sites = sites;
r_length = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_length;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_length = curr_sub_block->r_length;
curr_sub_block->r_length = r_length;
/*************����Ҫ��**************/
/**
r_size = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_size;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_size = curr_sub_block->r_size;
curr_sub_block->r_size = r_size;
reads = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].reads;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].reads = curr_sub_block->reads;
curr_sub_block->reads = reads;
**/
r_size_3_bit = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_size_3_bit;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_size_3_bit = curr_sub_block->r_size_3_bit;
curr_sub_block->r_size_3_bit = r_size_3_bit;
reads_3_bit = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].reads_3_bit;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].reads_3_bit = curr_sub_block->reads_3_bit;
curr_sub_block->reads_3_bit = reads_3_bit;
r_real_length = buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_real_length;
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].r_real_length = curr_sub_block->r_real_length;
curr_sub_block->r_real_length = r_real_length;
/*************����Ҫ��**************/
buffer_methy_out.sub_buffer[buffer_methy_out.sub_block_number].current_size = curr_sub_block->current_size;
///���Ӧ�÷����ٽ���֮����
///clear_methylation(curr_sub_block);
buffer_methy_out.sub_block_number++;
}
///�����Ҫ��curr_sub_block�Ľ���ŵ�������
inline void push_single_methy_buffer_pair(Pair_Methylation* curr_sub_block)
{
///����ռ�Ӧ����genome_cut+1
bitmapper_bs_iter* cut_index; ///���Ҫ����
Single_Methylation tmp_R; ///���Ҫ����
cut_index = buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].cut_index;
buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].cut_index = curr_sub_block->cut_index;
curr_sub_block->cut_index = cut_index;
///read1
tmp_R = buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].R[0];
buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].R[0] = curr_sub_block->R[0];
curr_sub_block->R[0] = tmp_R;
///read2
tmp_R = buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].R[1];
buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].R[1] = curr_sub_block->R[1];
curr_sub_block->R[1] = tmp_R;
buffer_methy_out_PE.sub_buffer[buffer_methy_out_PE.sub_block_number].current_size = curr_sub_block->current_size;
///���Ӧ�÷����ٽ���֮����
///clear_methylation(curr_sub_block);
buffer_methy_out_PE.sub_block_number++;
}
void finish_output_buffer()
{
if (output_methy == 0)
{
///���ҲҪ�ӻ�����
pthread_mutex_lock(&o_doneMutex);
buffer_out.all_buffer_end++;
if (buffer_out.all_buffer_end == THREAD_COUNT)
pthread_cond_signal(&o_flushCond);
pthread_mutex_unlock(&o_doneMutex);
}
else
{
///���ҲҪ�ӻ�����
pthread_mutex_lock(&o_doneMutex);
buffer_methy_out.all_buffer_end++;
if (buffer_methy_out.all_buffer_end == THREAD_COUNT)
pthread_cond_signal(&o_flushCond);
pthread_mutex_unlock(&o_doneMutex);
}
}
void finish_output_buffer_pair()
{
if (output_methy == 0)
{
///���ҲҪ�ӻ�����
pthread_mutex_lock(&o_doneMutex);
buffer_out.all_buffer_end++;
if (buffer_out.all_buffer_end == THREAD_COUNT)
pthread_cond_signal(&o_flushCond);
pthread_mutex_unlock(&o_doneMutex);
}
else
{
///���ҲҪ�ӻ�����
pthread_mutex_lock(&o_doneMutex);
buffer_methy_out_PE.all_buffer_end++;
if (buffer_methy_out_PE.all_buffer_end == THREAD_COUNT)
pthread_cond_signal(&o_flushCond);
pthread_mutex_unlock(&o_doneMutex);
}
}
void push_results_to_buffer(Output_buffer_sub_block* sub_block)
{
pthread_mutex_lock(&o_queueMutex);
///if_full_buffer
while (if_full_buffer())
{
///����������ź����ƺ����÷�
///��Ϊ���в�����һ����һ�߿�
pthread_cond_signal(&o_flushCond);
pthread_cond_wait(&o_stallCond, &o_queueMutex);
}
push_single_buffer(sub_block);
pthread_cond_signal(&o_flushCond);
pthread_mutex_unlock(&o_queueMutex);
}
void push_methy_to_buffer(Methylation* methy)
{
pthread_mutex_lock(&o_queueMutex);
///if_full_buffer
while (if_full_methy_buffer())
{
///����������ź����ƺ����÷�
///��Ϊ���в�����һ����һ�߿�
pthread_cond_signal(&o_flushCond);
pthread_cond_wait(&o_stallCond, &o_queueMutex);
}
push_single_methy_buffer(methy);
pthread_cond_signal(&o_flushCond);
pthread_mutex_unlock(&o_queueMutex);
clear_methylation(methy);
}
void push_methy_to_buffer_pair(Pair_Methylation* methy)
{
pthread_mutex_lock(&o_queueMutex);
///if_full_buffer
while (if_full_methy_buffer_pair())
{
///����������ź����ƺ����÷�
///��Ϊ���в�����һ����һ�߿�
pthread_cond_signal(&o_flushCond);
pthread_cond_wait(&o_stallCond, &o_queueMutex);
}
push_single_methy_buffer_pair(methy);
pthread_cond_signal(&o_flushCond);
pthread_mutex_unlock(&o_queueMutex);
clear_methylation_pair(methy);
}
void* pop_buffer(void*)
{
FILE* output_file = get_Ouput_Dec();
init_buffer_sub_block(&tmp_buffer_sub_block);
while (buffer_out.all_buffer_end<THREAD_COUNT)
{
pthread_mutex_lock(&o_queueMutex);
while (if_empty_buffer() && (buffer_out.all_buffer_end<THREAD_COUNT))
{
///����������ź����ƺ����÷�
///��Ϊ���в�����һ����һ�߿�
pthread_cond_signal(&o_stallCond);
pthread_cond_wait(&o_flushCond, &o_queueMutex);
}
if (!if_empty_buffer())
{
pop_single_buffer(&tmp_buffer_sub_block);
}
pthread_cond_signal(&o_stallCond);
pthread_mutex_unlock(&o_queueMutex);
if (tmp_buffer_sub_block.length != 0)
{
///����fwrite��fprintf����û����....�ٶ���
fprintf(output_file, "%s", tmp_buffer_sub_block.buffer);
}
}
while (buffer_out.sub_block_number>0)
{
buffer_out.sub_block_number--;
fprintf(output_file, "%s", buffer_out.sub_buffer[buffer_out.sub_block_number].buffer);