fquack is a DuckDB loadable extension written in Rust that streams FASTQ reads into analytical workflows. It registers a single table function, fquack(path), that returns one row per FASTQ record with columns for read metadata, nucleotide sequence, and ASCII-encoded quality scores.

This library is early development and my way of exploring Rust and expanding my understanding of DuckDB. Use at your own risk (For now)!

• Uses DuckDB's virtual table API (duckdb crate with vtab-loadable feature) so queries can treat reads as relational data.
• Packages the compiled shared library into a .duckdb_extension artifact for easy loading from DuckDB shells or applications.

• Rust toolchain (1.74 or newer recommended).
• Python 3 with venv support.
• GNU Make.
• DuckDB (for running queries against the extension).

Clone the repository with submodules:

git clone --recurse-submodules git@github.com:Scarzer/fquack.git
cd fquack

1. Configure the workspace (installs the DuckDB SQLLogic harness and records the host platform):

   make configure

2. Build a debug extension artifact:

   make debug

   The packaged binary is written to build/debug/extension/fquack/fquack.duckdb_extension.
3. For an optimized artifact, run:

   make release

   The release build is placed in build/release/extension/fquack/.

Launch DuckDB with unsigned extensions enabled, load the local artifact, and query a FASTQ file.

duckdb -unsigned

LOAD './build/debug/extension/fquack/fquack.duckdb_extension';

Create a tiny sample FASTQ (optional) and query it:

cat <<'EOF' > example.fastq
@read1
ACGT
+
!!!!
@read2
TTGC
+
####
EOF

SELECT metadata, sequence, quality
FROM fquack('example.fastq');

Output columns:

• metadata: FASTQ identifier (text after the leading @).
• sequence: nucleotide string (A/C/G/T/N).
• quality: ASCII-encoded quality scores as stored in the file.

To target a different DuckDB binary:

make clean_all
DUCKDB_TEST_VERSION=v1.3.2 make configure
make debug
make test_debug

Ensure that TARGET_DUCKDB_VERSION in Makefile matches the DuckDB crate versions in Cargo.toml to avoid ABI mismatches.

This extension is based off the rust extension template and draws heavily from the following projects:

• fqkit
• pcap_reader_bfe
• duckdb-file-tools
• seq_io