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DNASequence
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danger bug fix

This commit is contained in:
Zengtudor 2024-09-20 15:31:47 +08:00
parent 525c5e204e
commit 0e0febeb5f
2 changed files with 8 additions and 3 deletions
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1
src/main.cpp
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@ -30,6 +30,7 @@ int main()
//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); //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);
//这个函数在src/tools/dna里面 //这个函数在src/tools/dna里面
dna::open_file_and_calculate<(size_t)4*1024 * 1024 *1024 , (size_t)5e4+5>("filteredReads.txt", "reversedSequence.txt",reverseComplement); dna::open_file_and_calculate<(size_t)4*1024 * 1024 *1024 , (size_t)5e4+5>("filteredReads.txt", "reversedSequence.txt",reverseComplement);
// dna::open_file_and_calculate<(size_t)30, (size_t)5e4 + 5>("test.txt", "test.out.txt", reverseComplement);
}catch(const std::exception &e){ }catch(const std::exception &e){
zt::eprint( zt::eprint(

10
src/tools/dna.hpp
View File

@ -74,8 +74,10 @@ namespace dna {
Spent all_spent("All spent"); //自动计时器，给主函数计时 Spent all_spent("All spent"); //自动计时器，给主函数计时
unsigned int chunk_id = 0; unsigned int chunk_id = 0;
size_t last_buf_size = 0; size_t last_buf_size = 0;
while (input_file_stream.eof()==false) while (input_file_stream.eof()==false)
{ {
size_t recovered_size = 0;
Spent chunk_spent(zt::fmt("chunk_id:[",++chunk_id,"]")); Spent chunk_spent(zt::fmt("chunk_id:[",++chunk_id,"]"));
{ {
Spent chunk_read_spent(zt::fmt("read_chunk_id:[",chunk_id,"]")); Spent chunk_read_spent(zt::fmt("read_chunk_id:[",chunk_id,"]"));
@ -108,8 +110,10 @@ namespace dna {
} }
// lines=!lines; // lines=!lines;
output_file_stream.write(tmp_buf.data(), last_buf_size+end_pos+1); output_file_stream.write(tmp_buf.data(), last_buf_size+end_pos+1);
start_pos=end_pos+1;
recovered_size=end_pos+1;
}else{ }else{
THROW_RT_ERROR("DNA incompleteness") THROW_RT_ERROR("DNA incompleteness, chunk Size is too small !!")
} }
last_buf_size=0; last_buf_size=0;
} }
@ -152,12 +156,12 @@ namespace dna {
if(start_pos!=buf_len){ if(start_pos!=buf_len){
zt::print("Saving interrupt chunk_id[",chunk_id,"]\n"); 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)); std::memcpy(tmp_buf.data(),buf.data()+start_pos,(last_buf_size = buf_len-start_pos));
} }
{ {
Spent chunk_write_spent(zt::fmt("write_chunk_id:[",chunk_id,"] , ","[Wrote bytes] ",NAME_VALUE(start_pos))); 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); output_file_stream.write(buf.data()+recovered_size, start_pos-recovered_size);
} }