idba安装以及设置2023-11-15

https://github.com/loneknightpy/idba

conda安装

conda install -c bioconda idba

源代码安装

Extract the package, then use make to compile the source code.

$ ./configure
$ make

设置"fasta long read file"&"kmer"

设置输入文件的序列长度限制，以及最大kmer，默认的值不够用？如何在编译中设置更大范围。
fasta long read file
在设置文件改动数值

#/apps/idba-1.1.3/src/sequence/short_sequence.h
.....
#此处设置多少fasta read file就是多少
static const uint32_t kMaxShortSequence = 设置序列长度

.....

maximum kmer value

#/apps/idba-1.1.3/src/basic/kmer.h
.....
#这块计算比较复杂，
#我就直接把static const uint32_t kNumUint64的值翻番由4变成了8
#最大kmer就由原先的124变成了252.
    static const uint32_t kNumUint64 = 8;
    static const uint32_t kBitsForSize = ((kNumUint64 <= 2) ? 6 : ((kNumUint64 <= 8) ? 8 : 16));
    static const uint32_t kBitsForKmer = (kNumUint64 * 64 - kBitsForSize);
    static const uint32_t kMaxSize = kBitsForKmer / 2;

.....