Create a lazy table reference from a BED file

Streams a BED (Browser Extensible Data) file of genomic features as rows, one row per feature. Columns follow the BED specification in order: chrom, start, end, name, score, strand, thickStart, thickEnd, itemRgb, blockCount, blockSizes, blockStarts; any fields beyond the twelfth (a "BED N+" file) are read as strings named V13, V14, ... The column count is fixed by the first feature line and every later line must match it. Features stream one batch at a time, so a genome-scale interval set never fully materializes. Gzip-compressed files (.bed.gz) are read transparently. No data is read until collect() is called.

Usage

tbl_bed(path, batch_size = .DEFAULT_BATCH_SIZE, quiet = FALSE)

Arguments

path: Path to a .bed file, optionally gzip-compressed.
batch_size: Number of features per batch (default 65536).
quiet: If FALSE (default), report the feature count when the scan completes.

Value

A vectra_node object representing a lazy scan of the BED file.

Details

Fields are whitespace-delimited (tab or space), and blank lines, # comments, and UCSC track/browser directive lines are skipped. chrom, start, and end are required; start and end are integers (a non-integer there stops the scan). Optional integer fields (score, thickStart, thickEnd, blockCount) accept . or NA as missing. When the scan reaches the end of the file it reports the number of features read (suppress with quiet = TRUE).

Coordinates are read faithfully. BED start is 0-based and end is half-open (the first position past the feature), and both are returned exactly as stored — no coordinate is rewritten. Two features that abut (end of one equal to start of the next) share no base. To overlap-join BED tables with those half-open semantics — matching bedtools and GenomicRanges::findOverlaps() — pass closed = FALSE to interval_join(), which requires a strictly positive overlap and so does not pair abutting features:

peaks <- tbl_bed("peaks.bed")
genes <- tbl_bed("genes.bed")
interval_join(peaks, genes, start = "start", end = "end",
              by = "chrom", closed = FALSE)

Examples

f <- tempfile(fileext = ".bed")
writeLines(c("chr1\t100\t200\tfeatA\t0\t+",
             "chr1\t150\t400\tfeatB\t0\t-",
             "chr2\t500\t900\tfeatC\t0\t+"), f)
node <- tbl_bed(f, quiet = TRUE)
node |> filter(chrom == "chr1") |> collect()
unlink(f)