- BedTool.pair_to_pair(*args, **kwargs)¶
For convenience, the file or stream this BedTool points to is implicitly passed as the
Original BEDTools help::
Tool: bedtools pairtopair (aka pairToPair) Version: v2.30.0 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.