rduckhts_bam_bin_counts: Native Fixed-Width BAM/CRAM Bin Counts

In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

Native Fixed-Width BAM/CRAM Bin Counts

Description

Count read starts into fixed-width genomic bins with optional duplicate handling and optional per-bin GC and MAPQ summary statistics.

Usage

rduckhts_bam_bin_counts(
  con,
  path,
  bin_width,
  chrom = NULL,
  include_unmapped = FALSE,
  reference = NULL,
  index_path = NULL,
  mapq = 0,
  require_flags = 0,
  exclude_flags = 0,
  rmdup = "none",
  stats = NULL
)

Arguments

con	A DuckDB connection with DuckHTS loaded
path	Path to the input BAM or CRAM file
bin_width	Positive fixed bin width in bases
chrom	Optional chromosome name filter
include_unmapped	Logical. If 'TRUE', append one synthetic row for unmapped/no-coordinate records with 'chrom = "*"', and 'start', 'end', and 'bin_id' set to 'NA'.
reference	Optional reference FASTA path for CRAM input when required, and for reference-GC output when 'stats' includes '"gc"'
index_path	Optional explicit BAM/CRAM index path
mapq	Minimum mapping quality threshold applied after duplicate logic
require_flags	Required SAM flag mask
exclude_flags	Excluded SAM flag mask
rmdup	Duplicate handling mode: '"none"', '"flag"', or '"streaming"'
stats	Optional comma-separated subset of '"gc"' and '"mq"'

Value

A data frame with one row per fixed-width bin across the selected contig span, including zero-count bins, plus total, forward, reverse, and optional GC/MAPQ summary columns

Rduckhts documentation built on Oct. 25, 2026, 1:08 a.m.