pileup: bed vs. bedpe inference

[gfudenberg]

if a bedpe type file is provided, but columns are ['chrom', ' start', 'end', 'chrom1', 'start1', 'end1', 'chrom2', 'start2', 'end2'], pileup() silently defaults to on-diagonal pileup type, because the ['chrom', 'start', 'end'] are autodetected first.

potential solution:

• replace autodetection with a feature_type argument that specifies whether pileup should consider input dataframe as a bed or bedpe

cc @Phlya

[gfudenberg]

CLI seems to be a bit pickier about how features are provided!

https://github.com/open2c/cooltools/blob/6a7d1158c59457c63c8a032444f772fcd22766d1/cooltools/cli/pileup.py#LL178C1-L181C10

raise NotImplementedError(
            "Automatic detection of features format is not implemented yet. "
            "Please provide BED or BEDPE as --features-format"
        )

[nvictus]

We could also add a cols argument to customize the column names. Depending on feature_type, this would expect a length-3 or length-6 list of names.