Convert BAM/CRAM to a bgzipped BED bin-count file

Runs bam_convert() and writes the per-bin read counts to a bgzipped, tab-delimited BED file (four columns: chrom, start, end, count), then creates a tabix index (.tbi) alongside it via Rduckhts. This is the language-agnostic intermediate format for the RWisecondorX native pipeline; the file can be queried directly with duckhts/DuckDB or any tabix-aware tool.

Usage

bam_convert_bed(
  bam,
  bed,
  binsize = 5000L,
  mapq = 1L,
  require_flags = 0L,
  exclude_flags = 0L,
  rmdup = c("streaming", "none", "flag"),
  con = NULL,
  reference = NULL,
  index = TRUE
)

Arguments

bam

Path to an indexed BAM or CRAM file.

bed

Path for the output .bed.gz file (created or overwritten). The tabix index is written to paste0(bed, ".tbi").

binsize

Bin size in base pairs (default 5000).

mapq

Minimum mapping quality (default 1L).

require_flags

Integer bitmask; only reads with all bits set are kept (samtools -f). Default 0L (no requirement).

exclude_flags

Integer bitmask; reads with any bit set are dropped (samtools -F). Default 0L (nothing dropped).

rmdup

Duplicate-removal strategy passed to bam_convert().

con

Optional open DBI connection with duckhts already loaded. If NULL (default), a temporary in-memory DuckDB connection is created.

reference

Optional FASTA reference path for CRAM inputs.

index

Logical; when TRUE (default) a tabix index is created alongside the bgzipped output.

Value

bed (invisibly).

Details

Coordinates are 0-based half-open intervals matching the BED convention (start = bin_index * binsize, end = start + binsize). Chromosomes are written as 1–22, X, Y (no chr prefix) in numeric order. All bins are written, including those with a count of zero.

bgzip and tabix indexing are performed via Rduckhts::rduckhts_bgzip() and Rduckhts::rduckhts_tabix_index(), so no external tools are required.

See also

bam_convert(), bam_convert_npz(), wisecondorx_convert()

Examples

if (FALSE) { # \dontrun{
bam_convert_bed("sample.bam", "sample.bed.gz", binsize = 5000, rmdup = "streaming")
} # }