Read and combine multiple FASTQ 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_fastq_multi(
con,
table_name,
files,
mate_path = NULL,
interleaved = FALSE,
sequence_encoding = NULL,
quality_representation = NULL,
input_quality_encoding = NULL,
scan_mode = NULL,
.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.
- mate_path
Optional mate file path (for paired-end).
- interleaved
Logical; TRUE if file contains interleaved paired reads.
- sequence_encoding
Optional sequence encoding.
- quality_representation
Optional quality representation.
- input_quality_encoding
Optional input quality encoding override.
- scan_mode
Optional scan mode (
"auto"or"sequential").- .params
Optional data.frame with per-file parameter overrides.
- overwrite
Logical; if
TRUE, replace an existing table.