rduckhts_fastq: Create FASTQ Table

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

Create FASTQ Table

Description

Creates a DuckDB table from FASTQ files using the DuckHTS extension.

Usage

rduckhts_fastq(
  con,
  table_name,
  path,
  mate_path = NULL,
  interleaved = FALSE,
  sequence_encoding = NULL,
  quality_representation = NULL,
  input_quality_encoding = NULL,
  scan_mode = NULL,
  overwrite = FALSE
)

Arguments

con	A DuckDB connection with DuckHTS loaded
table_name	Name for the created table
path	Path to the FASTQ file
mate_path	Optional path to mate file for paired reads
interleaved	Logical indicating if file is interleaved paired reads
sequence_encoding	Character. Sequence encoding for the SEQUENCE column: "string" (default) returns decoded bases as VARCHAR; "nt16" returns raw htslib nt16 4-bit codes as UTINYINT[].
quality_representation	Character. Quality representation for the QUALITY column: "string" (default) returns canonical Phred+33 text; "phred" returns raw Phred values as UTINYINT[].
input_quality_encoding	Character. Input FASTQ quality encoding: "phred33" (default FASTQ convention), "auto", "phred64", or "solexa64".
scan_mode	Optional scan mode. Use "auto" (default extension behavior) or "sequential" to force raw streaming/counting instead of index-backed count paths.
overwrite	Logical. If TRUE, overwrites existing table

Value

Invisible TRUE on success

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