BWA源码阅读笔记（一）什么是nst_nt4_table

高通量数据比对讲究的就是一个快和准，因此大部分软件都是用C语言实现。BWA是目前基因组序列比对最常用的工具，由于自我感觉已经入门C语言，为了提高自己的水平，因此开始从源码角度学习李恒大神开发的BWA工具。

本次介绍的是bntseq.c开头这部分看起来强行凑代码量的表格，但本质上是一种用空间换时间哈希函数。

unsigned char nst_nt4_table[256] = {
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 5 /*'-'*/, 4, 4,
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
};

李恒利用该表格将ACGT/acgt转成0-3的数组，例如A,C,G,T,N的位置分别是65,67, 71,84,78, a,c,g,t对应97,99,103,116. 除了这个四个碱基外，其余都是大于4，对应N。

unsigned char nst_nt4_table[256] = {
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 5 /*'-'*/, 4, 4,
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 0(A), 4, 1(C),  4, 4, 4, 2(G),  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  3(T), 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 0(a), 4, 1(c),  4, 4, 4, 2(g),  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  3(t), 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
};

当然你可以写多个条件语句，来实现这种转换，例如下面的代码

    char nuc; 
    int c;
    switch (nuc){
    case tolower(nuc) == 'a'; c = 0; 
        break;
    case tolower(nuc) == 'c'; c = 1; 
        break;
    case tolower(nuc) == 'g'; c = 2; 
        break;
    case tolower(nuc) == 't'; c = 3; 
        break;
    default: c = 4;
        break;
    }

但是tolower涉及到加减运算，又会额外增加计算量。如果不用tolower，我们再加4个逻辑判断，那么每次将碱基转成数字平均为4次逻辑判断，在数据量很大的情况下，也是不小的负担。

而如果直接编码成长度为256数组，每次查询只要做一次计算，速度相当于提高了四倍。用额外的空间换取了速度的优势。