update
This commit is contained in:
parent
e25f75fe53
commit
5c4c7cd3f6
137
src/main.cpp
137
src/main.cpp
@ -5,15 +5,18 @@
|
||||
#include <exception>
|
||||
#include <filesystem>
|
||||
#include<fstream>
|
||||
#include <limits>
|
||||
#include <sstream>
|
||||
#include <stdexcept>
|
||||
#include<algorithm>
|
||||
#include"tools.hpp" // 自己写的库，在src/tools/tools.hpp当中，注意要使用C++23标准编译
|
||||
#include <cstring>
|
||||
#include <stdio.h>
|
||||
#include <string>
|
||||
#include <string_view>
|
||||
#include <type_traits>
|
||||
#include <unordered_map>
|
||||
#include <vector>
|
||||
|
||||
|
||||
// 这两个宏用来申请读入和读出流，实现反射并输出日志，获取申请流的变量名字
|
||||
@ -21,10 +24,11 @@
|
||||
#define OPEN_IFS_AND_CHECK(file_path,value_name)std::ifstream value_name(file_path);if(value_name.is_open()==false){std::stringstream ss;ss<<"cannot open input file stream : "<<file_path.filename();throw std::runtime_error(ss.str());}else{zt::print("Open input file stream to value ["#value_name"] ok , from [",file_path.filename(),"]\n");}
|
||||
|
||||
#define OPEN_OFS_AND_CHECK(file_path,value_name)std::ofstream value_name(file_path);if(value_name.is_open()==false){std::stringstream ss;ss<<"cannot open output file stream : "<<file_path.filename();throw std::runtime_error(ss.str());}else{zt::print("Open output file stream to value ["#value_name"] ok , from [",file_path.filename(),"]\n");}
|
||||
//最大DNA序列长度
|
||||
const size_t MAX_SIZE = 5e4+5;
|
||||
|
||||
void reverseComplement(auto &DNAsequence, const size_t buf_size) //注意这里使用引用DNA sequence，避免拷贝开销
|
||||
//最大DNA序列长度
|
||||
const size_t MAX_SIZE_PER_DNA = 5e4+5;
|
||||
|
||||
void reverseComplement(char *begin, char *end) //注意这里使用引用DNA sequence，避免拷贝开销
|
||||
{
|
||||
static const std::unordered_map<char, char> complement = { //这里使用查表的方式大大提高CPU速度，因为if分支CPU不容易命中缓存，需要使用查表加速
|
||||
{'A', 'T'}, {'a', 'T'},
|
||||
@ -33,12 +37,12 @@ void reverseComplement(auto &DNAsequence, const size_t buf_size) //注意这里
|
||||
{'G', 'C'}, {'g', 'C'}
|
||||
};
|
||||
|
||||
std::reverse(DNAsequence.begin(), DNAsequence.begin() + buf_size); //翻转DNA序列
|
||||
std::reverse(begin, end); //翻转DNA序列
|
||||
|
||||
for (std::remove_const_t<decltype(buf_size)> i = 0; i < buf_size; ++i) { //std::remove_const_t<decltype(buf_size)>意思是和buf_size相同的类型并去掉const
|
||||
auto it = complement.find(DNAsequence[i]);//查表并替换
|
||||
for (std::remove_const_t<decltype(begin)> i = begin; i < end; ++i) { //std::remove_const_t<decltype(buf_size)>意思是和buf_size相同的类型并去掉const
|
||||
auto it = complement.find(*i);//查表并替换
|
||||
if (it != complement.end()) [[likely]] {
|
||||
DNAsequence[i] = it->second;
|
||||
*i = it->second;
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -47,9 +51,9 @@ void reverseComplement(auto &DNAsequence, const size_t buf_size) //注意这里
|
||||
class Spent{ // 使用RAII原理的自动计时器，计算主函数运行时间，析构时自动输出
|
||||
private:
|
||||
const decltype(std::chrono::system_clock::now()) start;
|
||||
const std::string_view name;
|
||||
const std::string name;
|
||||
public:
|
||||
Spent(const std::string_view name)noexcept:start(std::chrono::system_clock::now()),name(name){
|
||||
Spent(const std::string name)noexcept:start(std::chrono::system_clock::now()),name(name){
|
||||
zt::print("[Timer: ",name,"]"," Start timing","\n");
|
||||
}
|
||||
~Spent()noexcept{
|
||||
@ -64,47 +68,120 @@ int main()
|
||||
try{
|
||||
//std::ios_base::sync_with_stdio(false); //加了没效果 //这里直接关掉就行了，不会影响读入，因为目前是一次性读入。开了反而会让日志输出变成全缓冲，不友好
|
||||
// using namespace std; // 别加，刚被坑了
|
||||
|
||||
Spent all_spent("All spent"); //自动计时器，给主函数计时
|
||||
|
||||
std::array<char,MAX_SIZE> buf;
|
||||
// std::array<char,MAX_SIZE> buf;
|
||||
|
||||
bool lines = 0; //使用布尔值加速
|
||||
|
||||
const auto get_lines_add = [&lines]() {
|
||||
bool old_value = lines; // 保存旧值
|
||||
lines = !lines; // 改变布尔值
|
||||
return old_value; // 返回旧值
|
||||
};
|
||||
|
||||
|
||||
std::filesystem::path input_path("filteredReads.txt"),output_path("reversedSequence.txt");
|
||||
|
||||
OPEN_IFS_AND_CHECK(input_path, input_file_stream) //创建输入和输出流
|
||||
OPEN_OFS_AND_CHECK(output_path, output_file_stream)
|
||||
|
||||
while (input_file_stream.getline(buf.data(),MAX_SIZE,'\n'))
|
||||
{
|
||||
// lines=!lines; //防止溢出
|
||||
const auto buf_len = strlen(buf.data());
|
||||
const std::string_view suffix("\n"); //设置一个每个DNA序列结尾的字符，这里是以\n换行来结尾
|
||||
if (lines == true){
|
||||
// output_file_stream << reverseComplement(buf) << endl;
|
||||
reverseComplement(buf,buf_len);
|
||||
}
|
||||
// buf+=suffix;
|
||||
for(std::remove_const_t<decltype(suffix.size())> i=0;i<suffix.size();i++){
|
||||
buf[buf_len+i] = suffix[i];
|
||||
}
|
||||
output_file_stream.write(buf.data(), buf_len+suffix.size()); // 写入文件
|
||||
lines=!lines; //bool取反
|
||||
}
|
||||
const size_t BUF_SIZE = (size_t)4 * 1024 * 1024 *1024; //4GB + 区块大小一点冗余 ///////////////////////////设置区块大小
|
||||
// const size_t BUF_SIZE = (size_t)400*1024*1024; //4GB + 一点冗余 // 测试用
|
||||
|
||||
std::vector<char> buf(BUF_SIZE); // 堆上分配可以大一点
|
||||
std::array<char, MAX_SIZE_PER_DNA> tmp_buf;//用于处理截断的DNA，直接在栈上申请
|
||||
|
||||
return 0;
|
||||
Spent all_spent("All spent"); //自动计时器，给主函数计时
|
||||
unsigned int chunk_id = 0;
|
||||
size_t last_buf_size = 0;
|
||||
while (input_file_stream.eof()==false)
|
||||
{
|
||||
Spent chunk_spent(zt::fmt("chunk_id:[",++chunk_id,"]"));
|
||||
{
|
||||
Spent chunk_read_spent(zt::fmt("read_chunk_id:[",chunk_id,"]"));
|
||||
input_file_stream.read(buf.data(),buf.size());
|
||||
}
|
||||
// lines=!lines; //防止溢出
|
||||
const auto buf_len = input_file_stream.gcount();
|
||||
|
||||
zt::print(NAME_VALUE(buf_len),"\n");
|
||||
|
||||
if(buf_len == std::numeric_limits<decltype(buf_len)>::max())[[unlikely]]{
|
||||
THROW_RT_ERROR("get input file stream read buf size failed\n")
|
||||
}
|
||||
|
||||
if(buf_len == 0)[[unlikely]]{
|
||||
break;
|
||||
}
|
||||
|
||||
const std::string_view buf_str_v(buf.data(),buf_len); //string_view是零拷贝，但是要注意悬垂引用
|
||||
|
||||
size_t start_pos = 0;
|
||||
size_t end_pos = 0;
|
||||
|
||||
if(last_buf_size>0)[[likely]]{
|
||||
Spent recovery_interrupt_spent(zt::fmt("recovery_interrupt [",chunk_id,"]"));
|
||||
if((end_pos=buf_str_v.find('\n',start_pos)) != std::string_view::npos)[[likely]]{
|
||||
std::memcpy(tmp_buf.data()+last_buf_size,buf.data(),end_pos+1);
|
||||
if(get_lines_add()){
|
||||
reverseComplement(tmp_buf.data(), tmp_buf.data()+last_buf_size+end_pos);
|
||||
}
|
||||
// lines=!lines;
|
||||
output_file_stream.write(tmp_buf.data(), last_buf_size+end_pos+1);
|
||||
}else{
|
||||
THROW_RT_ERROR("DNA incompleteness")
|
||||
}
|
||||
last_buf_size=0;
|
||||
}
|
||||
|
||||
{
|
||||
Spent calculate_spent(zt::fmt("calculate_chunk_id:[",chunk_id,"]"));
|
||||
|
||||
while((end_pos=buf_str_v.find('\n',start_pos)) != std::string_view::npos){
|
||||
if(get_lines_add()){
|
||||
reverseComplement(buf.data()+start_pos, buf.data()+end_pos);
|
||||
}
|
||||
// lines=!lines;
|
||||
start_pos=end_pos+1;
|
||||
}
|
||||
}
|
||||
|
||||
if(start_pos!=buf_len){
|
||||
zt::print("Saving interrupt chunk_id[",chunk_id,"]\n");
|
||||
std::memcpy(tmp_buf.data(),buf.data()+start_pos+1,(last_buf_size = buf_len-start_pos-1));
|
||||
}
|
||||
{
|
||||
Spent chunk_write_spent(zt::fmt("write_chunk_id:[",chunk_id,"] , ","[Wrote bytes] ",NAME_VALUE(start_pos)));
|
||||
output_file_stream.write(buf.data(), start_pos);
|
||||
}
|
||||
// zt::print("[Wrote bytes] ",NAME_VALUE(start_pos),"\n");
|
||||
// const std::string_view suffix("\n"); //设置一个每个DNA序列结尾的字符，这里是以\n换行来结尾
|
||||
|
||||
|
||||
// if (lines == true){
|
||||
// // output_file_stream << reverseComplement(buf) << endl;
|
||||
// reverseComplement(buf,buf_len);
|
||||
// }
|
||||
// // buf+=suffix;
|
||||
// for(std::remove_const_t<decltype(suffix.size())> i=0;i<suffix.size();i++){
|
||||
// buf[buf_len+i] = suffix[i];
|
||||
// }
|
||||
// output_file_stream.write(buf.data(), buf_len+suffix.size()); // 写入文件
|
||||
|
||||
}
|
||||
|
||||
}catch(const std::exception &e){
|
||||
zt::eprint(
|
||||
"Caught an error because:\n",
|
||||
"\t",NAME_VALUE(e.what()),"\n"
|
||||
"Closing\n"
|
||||
);
|
||||
throw e;
|
||||
}catch(...){
|
||||
zt::eprint(
|
||||
"Caught an unknown error :\n",
|
||||
"Closing\n"
|
||||
);
|
||||
throw;
|
||||
}
|
||||
return -1;
|
||||
}
|
||||
|
||||
@ -3,6 +3,8 @@
|
||||
#include <iostream>
|
||||
#include <ostream>
|
||||
#include <sstream>
|
||||
#include <string>
|
||||
#include <utility>
|
||||
|
||||
#define NAME_VALUE(v)#v," : ",(v)
|
||||
|
||||
@ -70,6 +72,14 @@ namespace zt {
|
||||
return;
|
||||
}
|
||||
|
||||
template<class ...Args>
|
||||
inline std::string fmt(Args&&... args) {
|
||||
std::ostringstream oss;
|
||||
(oss << ... << std::forward<Args>(args));
|
||||
return oss.str();
|
||||
}
|
||||
|
||||
#define THROW_RT_ERROR(why)throw std::runtime_error(zt::fmt("[FILE:",__FILE__,"] [LINE:",__LINE__,"] why:",why));
|
||||
// template <class ...Args>
|
||||
// inline void check_fstream_isopen(const Args&...args)noexcept(false){
|
||||
// bool is_open=true;
|
||||
|
||||
Loading…
Reference in New Issue
Block a user