Read multiple BAM/SAM files into a DuckDB table — rduckhts_bam

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.