The Daily WTF

As we frequently observe, code in scientific applications tends not to have the best code quality. And it’s not hard to understand why: a researcher is frequently trying to take a wholistic understanding of a complicated problem domain and turn it into code. Software engineering, on the other hand, teaches us to break that wholistic picture up into little parts that we glue back together. The latter approach produces better code, but requires a lot of thinking about the structure of code, which is a whole layer on top of that wholistic understanding.

Which brings us to Plink, a C program Oliver R has had to work with. It analyzes genetic variance data. It also has a method with this signature:

int32_t plink(char* outname, char* outname_end, char* bedname, char* bimname, char* famname, char* cm_map_fname, char* cm_map_chrname, char* phenoname, char* extractname, char* excludename, char* keepname, char* removename, char* keepfamname, char* removefamname,

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