Zengtudor
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DNASequence
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update

This commit is contained in:
Zengtudor 2024-09-18 23:12:26 +08:00
parent 800560693b
commit f19ad2d057
1 changed files with 23 additions and 21 deletions
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44
src/main.cpp
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@ -10,6 +10,7 @@
#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>
@ -24,7 +25,7 @@
//最大DNA序列长度
const size_t MAX_SIZE = 5e4+5;
void reverseComplement(std::array<char, MAX_SIZE> &DNAsequence, const size_t buf_size) //注意这里使用引用DNA sequence，避免拷贝开销
void reverseComplement(std::string &DNAsequence, const size_t buf_size) //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'},
@ -63,14 +64,17 @@ int main()
{
try{
std::ios_base::sync_with_stdio(false); //加了没效果
using namespace std;
// 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;
std::string buf;
buf.reserve(MAX_SIZE);//注意提前扩容
unsigned long long lines = 0;
filesystem::path input_path("filteredReads.txt"),output_path("reversedSequence.txt");
std::filesystem::path input_path("filteredReads.txt"),output_path("reversedSequence.txt");
// ifstream input_file_stream(input_path);
// ofstream output_file_stream(output_path);
@ -78,30 +82,28 @@ int main()
OPEN_OFS_AND_CHECK(output_path, output_file_stream)
// string l = "";
auto now_buf_pos = input_file_stream.tellg();
const auto get_buf_len = [&now_buf_pos,&input_file_stream,&buf](){
if(const auto new_buf_pos = input_file_stream.tellg(); new_buf_pos!=-1)[[likely]]{
const auto old_buf_pos = now_buf_pos;
now_buf_pos = new_buf_pos;
// auto ret = new_buf_pos - old_buf_pos;
return (unsigned long long)(new_buf_pos - old_buf_pos);
}else{
return strlen(buf.data());
}
};
// auto now_buf_pos = input_file_stream.tellg();
// const auto get_buf_len = [&now_buf_pos,&input_file_stream,&buf](){
// if(const auto new_buf_pos = input_file_stream.tellg(); new_buf_pos!=-1)[[likely]]{
// const auto old_buf_pos = now_buf_pos;
// now_buf_pos = new_buf_pos;
// // auto ret = new_buf_pos - old_buf_pos;
// return (unsigned long long)(new_buf_pos - old_buf_pos);
// }else{
// return strlen(buf.data());
// }
// };
while (input_file_stream.getline(buf.data(),MAX_SIZE,'\n'))
{
int m = lines%2;
const auto buf_len = get_buf_len();
// const auto buf_len = get_buf_len();
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 (m == 1){
// output_file_stream << reverseComplement(buf) << endl;
reverseComplement(buf,buf_len);
reverseComplement(buf,buf.size());
}
for(int i=0;i<suffix.size();i++){
buf[buf_len+i]=suffix[i]; // 将末尾增加字符追加到结尾。注意不能过长超过MAX_SIZE
}
output_file_stream.write(buf.data(), buf_len+suffix.size()); // 写入文件
buf+=suffix;
output_file_stream.write(buf.data(), buf.size()); // 写入文件
lines++;
}