rduckhts_pileup: Create BAM Pileup Table

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

Create BAM Pileup Table

Description

Creates a DuckDB table from a region-scoped BAM pileup using the DuckHTS extension. This is a compact base/quality pileup view backed by htslib's pileup engine; it is not samtools mpileup text parity.

Usage

rduckhts_pileup(
  con,
  table_name,
  path,
  region,
  index_path = NULL,
  min_mapq = 0,
  flag_mask = 1796,
  overwrite = FALSE
)

Arguments

con	A DuckDB connection with DuckHTS loaded
table_name	Name for the created table
path	Path to the BAM file
region	Required genomic region (e.g., "chr1:1000-2000")
index_path	Optional explicit path to the BAM index (.bai/.csi)
min_mapq	Minimum mapping quality to include in the pileup
flag_mask	Bitmask of SAM flags to exclude before pileup construction. The default 1796 matches samtools depth-style filtering of unmapped, secondary, QC-fail, and duplicate reads.
overwrite	Logical. If TRUE, overwrites existing table

Value

Invisible TRUE on success

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