Generating mutations with WGSim

[dkhavari]

I've just started using WGSim, and I'm trying to mutate the data a specified amount (eg: 300 bp using only simple point mutations) of an entire genome, and then get reads for it.

Apparently wgsim_mut_diref is supposed to be the way to do this, but the documentation is pretty minimalistic, and I am confused as to what exactly they are looking for as arguments:

void wgsim_mut_diref(const kseq_t *ks, int is_hap, mutseq_t *hap1, mutseq_t *hap2)

From my understanding, the arguments should be: my_input_file, 0 or 1, output_file_1, output_file_2. Where is the argument for mutation rate/base pairs mutated?

Here's the page with the actual source code, any help would be appreciated.

https://github.com/lh3/wgsim/blob/master/wgsim.c

Best,
David