49 lines
1.8 KiB
C++
49 lines
1.8 KiB
C++
#include "dna.hpp"
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//注意，这个函数会被并行执行，请只访问begin<=i<end之间的内容，以免出现数据竞争导致程序异常
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void reverseComplement(char *begin, char *end)
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{
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//注意end是开区间，不能访问end
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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
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{'A', 'T'}, {'a', 'T'},
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{'T', 'A'}, {'t', 'A'},
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{'C', 'G'}, {'c', 'G'},
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{'G', 'C'}, {'g', 'C'}
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};
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std::reverse(begin, end); //翻转DNA序列
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for (ptrdiff_t i = 0; i < (end - begin); ++i) {
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static int _ = (zt::print(NAME_VALUE(omp_get_num_threads()),"\n"),0); // 打印线程数量
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auto it = complement.find(begin[i]);
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if (it != complement.end()) {
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begin[i] = it->second;
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}
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}
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}
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int main()
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{
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try{
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//原理是这里定义处理函数，将函数传入dna::open_file_and_calculate，在open_file_and_calculate中会调用传入的函数
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//参数列表 <文件分块内存大小，单个DNA序列最长大小>("输入文件名","输出文件名",序列处理函数);
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//这个函数在src/tools/dna里面
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dna::open_file_and_calculate<(size_t)4*1024 * 1024 *1024 , (size_t)5e4+5>("filteredReads.txt", "reversedSequence.txt",reverseComplement);
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// dna::open_file_and_calculate<(size_t)30, (size_t)5e4 + 5>("test.txt", "test.out.txt", reverseComplement);
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}catch(const std::exception &e){
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zt::eprint(
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"Caught an error because:\n",
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"\t",NAME_VALUE(e.what()),"\n"
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"Closing\n"
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);
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throw e;
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}catch(...){
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zt::eprint(
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"Caught an unknown error :\n",
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"Closing\n"
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);
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throw;
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}
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}
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