2024-09-19 02:52:17 +00:00
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# 注意！
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> ***请详细阅读xmake.lua项目配置文件，可能涉及到性能优化和计算精度的问题***
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2024-09-18 06:52:32 +00:00
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# DNASequence
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2024-09-18 09:21:55 +00:00
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[提问者问题原文链接](https://www.zhihu.com/question/36143261/answer/3624848144)
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2024-09-18 09:23:24 +00:00
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## 代码逻辑介绍
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2024-09-18 09:21:55 +00:00
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DNASequence处理
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DNA是双链的，互为互补链，对DNA样本进行测序时不能确认测出的是哪条链，所以就把所有DNA片段的互补链全算出来，和原文件放在一起组装。
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2024-09-19 02:27:29 +00:00
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> 输入格式：只是演示样例，不保证其生物上的准确性，默认最大dna序列长度支持5e4，可自行修改代码扩容
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2024-09-19 02:29:22 +00:00
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>
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> 程序将会处理类似以下若干条dna序列
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2024-09-19 02:27:29 +00:00
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```
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@SRR13280199.1 1 length=32
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ACGTACACATTGCTGTCTGCTGAACCACCTAG
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```
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2024-09-18 09:27:32 +00:00
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## 关于如何构建本项目
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> 请确保安装了构建工具xmake，和任意C++构建工具并将路径添加到了PATH目录
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[如何安装xmake?链接](https://gitee.com/tboox/xmake#%E5%AE%89%E8%A3%85)
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```bash
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2024-09-18 10:47:32 +00:00
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#编译 -v 表示 verbose 输出详细编译信息具体说明去上面的xmake链接看看
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2024-09-18 09:27:32 +00:00
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xmake -v
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# 运行
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xmake r
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2024-09-18 10:47:32 +00:00
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2024-09-18 10:48:56 +00:00
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# 生成 visual studio 文件夹，点进去打开sln文件即可使用visual studio编辑和调试，很方便
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2024-09-18 10:47:32 +00:00
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xmake project -k vsxmake
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2024-09-18 09:27:32 +00:00
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```
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2024-09-18 11:15:24 +00:00
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2024-09-18 10:59:30 +00:00
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## 性能展示
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2024-09-19 02:15:54 +00:00
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> 什么环境下性能最好？
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> 经过测试，在windows环境下，前端使用mingw，后端使用llvm，也就是clang的时候性能最好
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2024-09-19 02:18:37 +00:00
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>
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> 可以酌情开启xmake.lua中的avx512加速
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2024-09-19 02:15:54 +00:00
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2024-09-18 11:15:24 +00:00
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> perf
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```
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Samples: 31K of event 'task-clock:ppp', Event count (approx.): 7866750000
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Overhead Command Shared Object Symbol
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90.39% test [unknown] [k] 0xffffffffa84435e1
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5.48% test test [.] reverseComplement(std::array<char, 50005ul>&, unsigned long)
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1.58% test [unknown] [k] 0xffffffffc06abd30
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0.59% test [unknown] [k] 0xffffffffa83ab787
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0.51% test [unknown] [k] 0xffffffffa842aee0
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```
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> 800MB fastq DNA 序列处理性能展示
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```
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[Timer: All spent] Start timing
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Open input file stream to value [input_file_stream] ok , from ["filteredReads.txt"]
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Open output file stream to value [output_file_stream] ok , from ["reversedSequence.txt"]
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Undergoing transformation
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[Timer: All spent] Stop timing , using 5960ms
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```
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2024-09-18 09:27:32 +00:00
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2024-09-18 09:23:24 +00:00
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## 关于版权
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2024-09-19 02:29:22 +00:00
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本项目算法版权归提问者所有，可不遵循开源协议，其它人使用请遵循开源协议，或者欢迎咨询我
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