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
1796matches samtools depth-style filtering of unmapped, secondary, QC-fail, and duplicate reads.- overwrite
Logical. If TRUE, overwrites existing table