Crate rsomics_bed_multiinter 

Multi-file interval intersection depth sweep.

Algorithm

For each position in the genome, reports how many of the N input BED files have at least one interval covering that position. Uses a coordinate-sweep (priority-queue over start/end events) per chromosome, emitting a row for every contiguous run of constant depth.

Output columns (tab-separated):

chrom  start  end  depth  list  file1  file2  ...  fileN

• depth: number of files with coverage at this position.
• list: comma-separated names (1-based indices, or -names labels) of covering files; "none" when depth = 0.
• file1..fileN: 1 if that file has coverage, 0 otherwise.

All input files must be sorted by chrom then start. Chromosomes are processed in the order they first appear across files (matching bedtools).

Reference

BEDTools multiinter — Quinlan & Hall (2010). Bioinformatics 26(6): 841–842. DOI: 10.1093/bioinformatics/btq033

Functions

multiinter

Run the multi-interval intersection sweep.