From 7c8fa8de850f5d0e4916c288abd58a53fba8986d Mon Sep 17 00:00:00 2001
From: Zengtudor <zengtudor@outlook.com>
Date: Fri, 20 Sep 2024 11:44:13 +0800
Subject: [PATCH] update

---
 .gitignore        |  3 ++-
 src/main.cpp      | 11 ++---------
 src/tools/dna.hpp | 34 +++++++++++++++++++++++++++++-----
 xmake.lua         |  2 +-
 4 files changed, 34 insertions(+), 16 deletions(-)

diff --git a/.gitignore b/.gitignore
index 3b76c95..c65c76f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,5 @@
 build
 filteredReads.txt
 reversedSequence.txt
-vsxmake*
\ No newline at end of file
+vsxmake*
+*.txt
\ No newline at end of file
diff --git a/src/main.cpp b/src/main.cpp
index e4c426c..beb5f44 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -10,15 +10,8 @@ void reverseComplement(char *begin, char *end)
         {'G', 'C'}, {'g', 'C'}
     };
 
-    // std::reverse(begin, end); //翻转DNA序列
-    // 并行翻转序列 //似乎没用
-    #pragma omp parallel for
-    for (ptrdiff_t i = 0; i < (end - begin) / 2; ++i) {
-        std::swap(begin[i], begin[(end - begin) - i - 1]);
-    }
-
-    // 并行查表替换
-    #pragma omp parallel for
+    std::reverse(begin, end); //翻转DNA序列
+    
     for (ptrdiff_t i = 0; i < (end - begin); ++i) {
         static int _ = (zt::print(NAME_VALUE(omp_get_num_threads()),"\n"),0); // 打印线程数量
         auto it = complement.find(begin[i]);
diff --git a/src/tools/dna.hpp b/src/tools/dna.hpp
index 7a4fd57..25cb1dc 100644
--- a/src/tools/dna.hpp
+++ b/src/tools/dna.hpp
@@ -117,13 +117,37 @@ namespace dna {
             {
                 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); //我想要这个函数并行优化
+                #pragma omp parallel
+                #pragma omp single
+                {
+                    while ((end_pos = buf_str_v.find('\n', start_pos)) != std::string_view::npos) {
+                        char *start = buf.data() + start_pos;
+                        char *end = buf.data() + end_pos;
+
+                        // 确保每个任务只操作属于它的独立数据
+                        if (get_lines_add()) {
+                            // 为每一块数据创建一个任务
+                            #pragma omp task firstprivate(start, end)
+                            {
+                                reverseComplement(start, end); // 任务内处理反转互补
+                            }
+                        }
+
+                        start_pos = end_pos + 1;
                     }
-                    // lines=!lines;
-                    start_pos=end_pos+1;
+
+                    // 等待所有任务完成
+                    #pragma omp taskwait
                 }
+
+
+                // 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); //我想要这个函数并行优化
+                //     }
+                //     // lines=!lines;
+                //     start_pos=end_pos+1;
+                // }
             }
             
             if(start_pos!=buf_len){
diff --git a/xmake.lua b/xmake.lua
index 132ed5e..4bc8bf7 100644
--- a/xmake.lua
+++ b/xmake.lua
@@ -15,7 +15,7 @@ if is_mode("release")then
 end
 
 if is_plat("windows")then 
-    add_cxxflags("/openmp")
+    add_cxxflags("/openmp:llvm")
 elseif is_plat("linux") or is_plat("mingw") or is_plat("clang")then 
     add_cxxflags("-fopenmp")
     add_ldflags("-fopenmp")