pybedtools.bedtool.BedTool.count_hits

BedTool.count_hits(interval: Interval, same_strand: bool = False, overlap: float = 0.0) → int

Return the number of intervals that overlap interval.

Calls the count_hits method of an IntervalFile. Returns the number of valid hits in this BedTool that overlap interval.

Require that overlaps have the same strand with same_strand=True.

Notes:

If this current BedTool is generator-based, it will be converted into a file first.

If this current BedTool refers to a BAM file, it will be converted to a BED file first using default arguments. If you don’t want this to happen, please convert to BED first before using this method.