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"`