Convert SAM/BAM/CRAM reader output to Parquet with DuckHTS metadata — rduckhts_bam_convert

Thin DBI wrapper around extension macro `duckhts_bam_convert_parquet_sql(...)`.

Usage

rduckhts_bam_convert_parquet(
  con,
  path,
  output,
  columns = NULL,
  region = NULL,
  index_path = NULL,
  reference = NULL,
  standard_tags = FALSE,
  auxiliary_tags = FALSE,
  sequence_encoding = NULL,
  quality_representation = NULL,
  cigar_representation = NULL,
  decompression_threads = 2,
  where = NULL,
  compression = "zstd",
  row_group_size = 100000L,
  partition_by = NULL,
  include_metadata = TRUE,
  header_text = NULL,
  metadata = NULL,
  metadata_json_file = NULL,
  write_format_version = "1",
  overwrite = FALSE
)

Arguments

con: A DuckDB connection with DuckHTS loaded.
path: Path or URI to the input SAM/BAM/CRAM file.
output: Path to the output Parquet file or partitioned directory.
columns: Optional character vector of columns to include. Defaults to all columns.
region: Optional genomic region string for indexed inputs.
index_path: Optional explicit index path.
reference: Optional reference FASTA path for CRAM.
standard_tags: Logical; include typed standard SAM tag columns.
auxiliary_tags: Logical; include non-standard auxiliary tags as a map.
sequence_encoding: Optional sequence encoding (`"string"` or `"nt16"`).
quality_representation: Optional quality representation (`"string"` or `"phred"`).
cigar_representation: Optional CIGAR representation (`"string"` or `"binary"`).
decompression_threads: Integer htslib decompression worker threads.
where: Optional SQL predicate applied to the reader output before conversion.
compression: Parquet compression, default `"zstd"`.
row_group_size: Parquet row group size.
partition_by: Optional character vector of output partition columns.
include_metadata: Logical; include DuckHTS Parquet KV metadata.
header_text: Optional corrected header text to store instead of the source header.
metadata: Optional named list/vector of extra metadata. This is the primary CRAN/offline-safe path for arbitrary metadata; values with the same names as DuckHTS defaults override the default values.
metadata_json_file: Optional path to a JSON file containing a top-level object of extra metadata. This requires DuckDB's `json` extension to be available when the conversion SQL is generated; otherwise DuckDB will report its normal missing-extension error. Use `metadata` for offline-safe metadata.
write_format_version: DuckHTS Parquet write-format version string.
overwrite: Logical; replace an existing output path. The wrapper checks existence through DuckDB `glob(...)` where possible and passes the same flag to DuckDB `COPY` for partitioned-output overwrite handling.

Value

Invisibly returns `output`.