Add store_bdg, SPMR, broad parameters for calling peaks using MACS3

[beyondpie]

Hi Kai,

I add three parameters for peak calling.

1. On bed graph generation:

   • SPMR and store_bdg, I open the two parameters since we notice that MACS2/3 can generate the smoothed bedgraphs for our later deep learning model usage.

2. On broad peak calling:

   • add broad to allow broad peak calling. We typically use this for broad peak calling on some histone modifications.

But I am not sure if this is enough for the peak calling function since I notice that you actually have a rust layer for the real task. Another question I have: there is nomodel parameter in the list. According the MACS3 README, it seems to be needed for extsize parameter.

By default, I set all of them false in order to keep the default behavior of your function.

Thanks! Songpeng