Are there filter options available for pileup?

[Crispy13]

In pysam, there are some options for filtering, min base quality, stepper, mapping quality, ignore overlaps .. etc.

Are there any options available for pileup function?

Thanks.

[dlaehnemann]

From how this sounds (I am not familiar with the functions in pysam), there are no such convenience functions in rust-htslib. But you should be able to achieve any kind of filtering that you want by digging into the docs:

Are you aware of the general docs right here, which provide some examples of how to filter alignments in a pileup (a bit further down):
https://docs.rs/rust-htslib/0.44.1/rust_htslib/#

Otherwise, there are infos on Alignments and Pileup(s) here:
https://docs.rs/rust-htslib/0.44.1/rust_htslib/bam/pileup/index.html

And finally, all the stuff you can do on a Record will probably help you filtering them (probably even before putting them into a pileup):
https://docs.rs/rust-htslib/0.44.1/rust_htslib/bam/record/struct.Record.html

[Crispy13]

Could you give a tiny example for the last part?

[davidmasp]

I am not super well versed in neither rust or C so excuse my ignorance if I am missing smth obvious.

Just to update a bit more the context from @Crispy13's question. The pileup function in pysam does have multiple options (see here). One of them is for instance ignore_overlaps that mimics the -x option in samtools.

pysam feels more like samtools so I understand there's no feature parity with rust_htslib. However, as far as I can tell from the pysam code and the samtools code, this functionality exists in htslib (see here) not in either library.

So my broader question is, can we access such functionality (i.e. ignoring overlaps) within rust_htslib? or what is the easiest path to do so?

[davidmasp]

Digging a bit more there seems to be bindings to the function that they use in samtools, here. I think it's a bit over my skill level though.