pybedtools.bedtool.BedTool.pair_to_pair

BedTool.pair_to_pair(*args, **kwargs)

Wraps bedtools pairtopair.

For convenience, the file or stream this BedTool points to is implicitly passed as the -a argument to pairToPair

Original BEDTools help::

Tool:    bedtools pairtopair (aka pairToPair)
Version: v2.31.1
Summary: Report overlaps between two paired-end BED files (BEDPE).

Usage:   bedtools pairtopair [OPTIONS] -a <BEDPE> -b <BEDPE>

Options: 
        -f      Minimum overlap required as fraction of A (e.g. 0.05).
                Default is 1E-9 (effectively 1bp).

        -type   Approach to reporting overlaps between A and B.

                neither Report overlaps if neither end of A overlaps B.
                either  Report overlaps if either ends of A overlap B.
                both    Report overlaps if both ends of A overlap B.
                notboth Report overlaps if one or neither of A's overlap B.
                - Default = both.

        -slop   The amount of slop (in b.p.). to be added to each footprint of A.
                *Note*: Slop is subtracted from start1 and start2
                        and added to end1 and end2.

                - Default = 0.

        -ss     Add slop based to each BEDPE footprint based on strand.
                - If strand is "+", slop is only added to the end coordinates.
                - If strand is "-", slop is only added to the start coordinates.
                - By default, slop is added in both directions.

        -is     Ignore strands when searching for overlaps.
                - By default, strands are enforced.

        -rdn    Require the hits to have different names (i.e. avoid self-hits).
                - By default, same names are allowed.

Refer to the BEDTools manual for BEDPE format.