rduckhts_bam_multi: Read multiple BAM/SAM files into a DuckDB table

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

Read multiple BAM/SAM files into a DuckDB table

Description

Read and combine multiple BAM/SAM files via UNION ALL BY NAME, materialising the result as a DuckDB table. Each row includes a filename column identifying its source file.

Usage

rduckhts_bam_multi(
  con,
  table_name,
  files,
  region = NULL,
  index_path = NULL,
  reference = NULL,
  standard_tags = FALSE,
  auxiliary_tags = FALSE,
  sequence_encoding = NULL,
  quality_representation = NULL,
  cigar_representation = NULL,
  scan_mode = NULL,
  decompression_threads = 2,
  .params = NULL,
  overwrite = FALSE
)

Arguments

con	A DBI connection to DuckDB with the duckhts extension loaded.
table_name	Name of the DuckDB table to create.
files	Character vector of file paths or glob patterns.
region	Optional region string (e.g. "chr1:1-1000").
index_path	Optional index file path.
reference	Optional reference FASTA path (for CRAM).
standard_tags	Logical; include standard SAM tag columns.
auxiliary_tags	Logical; include auxiliary tag map column.
sequence_encoding	Optional sequence encoding (e.g. "nt16").
quality_representation	Optional quality representation.
cigar_representation	Optional CIGAR representation; use "binary" for packed BAM operations.
scan_mode	Optional scan mode ("auto" or "sequential").
decompression_threads	Integer. Number of htslib decompression worker threads per file handle. Default 2. Use 0 to disable worker threads.
.params	Optional data.frame with per-file parameter overrides. Must contain a file column; other columns override uniform parameters. NA values use the uniform default.
overwrite	Logical; if TRUE, replace an existing table.

Value

Invisible TRUE on success.

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