CRAM reader output to Parquet with DuckHTS...
In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

rduckhts_bam_convert_parquet

R Documentation

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

Description

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.