Make mpileup coverage parameter configurable

[messersc]

Hi,

we are using EBFilter successfully, but we were recently running into trouble with some data that has very high coverage in some regions, i.e. low complexity regions like described in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271055/

Variants in the regions should be caught by EBfilter easily I guess, but we are running into trouble with the running times of the filtering. One bottleneck that we notice is the mpileup on the normals allows for a huge depth:

https://github.com/Genomon-Project/EBFilter/blob/devel/lib/ebfilter/process_vcf.py#L64

Would it be possible to make this user configurable? Even setting it to e.g. 10000, I can't imagine there would be a huge penalty in sensitivity.

We'd be grateful for any advice,
Best regards,
Clemens