Ryan Dale
Ryan Dale
See discussion in #215
Interesting, I agree this would be useful, but such magic does not currently exist in this package! I think the first missing piece would be to handle splicing properly, I...
Yep, good idea. Did you hit this with `genome_coverage` specifically or with another method?
#213 adds some documentation. I will try implementing something like https://github.com/daler/pybedtools/issues/110#issuecomment-206426464, xref #167
The VCF parser in pybedtools is pretty bare-bones: https://github.com/daler/pybedtools/blob/master/pybedtools/cbedtools.pyx#L671 However the calls out to bedtools should not be affected by this. I think I'd like to move to proper VCF...
Ah, thanks @kyleabeauchamp, good to know.
Good idea. I probably wouldn't use this myself, but it should be easy to add and might make the package more useful to others. I think the interaction between S3...
A while ago I did a major overhaul on the randomization stuff, implementing a new method (`BedTool._randomintersection` rather than `BedTool.randomintersection`) that fixed this. Looks like I never made this method...
Yeah, that's probably best. I still need to do a little more cleaning up and "officially" deprecate the old randomstats method; when that happens the genome_fn will be required.
Sure. Implementation-wise, would you rather create your own pool and use it for various parallel calls like ``` python mypool = multiprocessing.Pool(25) bt.randomstats(_orig_pool=mypool, *args, **kwargs) bt.random_op(_orig_pool=mypool, *args, **kwargs) bt.random_jaccard(_orig_pool=mypool, *args,...