FragmentIndex


class chr3d.peak_based.purifying.FragmentIndex(
    bed_path: str,
)

In-memory index of restriction fragments for fast overlap lookup.

Uses bisect for O(log N) overlap queries against a sorted interval list. Chromosomes are stored in separate lists to avoid cross-chromosome comparisons.

Parameters

Parameter	Type	Description
bed_path	`str`	Path to BED file with restriction fragments

Methods

find_overlapping


def find_overlapping(
    self,
    chrom: str,
    start: int,
    end: int,
) -> Optional[Tuple[int, int, int]]

Find a fragment overlapping the interval [start, end) on chrom.

Parameters:

Parameter	Type	Description
chrom	`str`	Chromosome name
start	`int`	Interval start position (0-based)
end	`int`	Interval end position (exclusive)

Returns:

Optional[Tuple[int, int, int]] — (start, end, frag_idx) of the overlapping fragment, or None if no overlap.