fraq
Bioc currentA High-Throughput and Extensible Toolkit for Processing FASTQ Data
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
High-throughput extensible toolkit for processing FASTQ data. The goal of this package is to empower users to quickly build out small programmatic 'kernels' to define any FASTQ processing task they may need. Builds on Intel TBB’s flow graph to orchestrate concurrent I/O and data processing; throughput can be as fast as compression and disk speed allows. The package also ships with a suite of predefined kernels for common FASTQ tasks.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
1414 21 exported
Complexity
2.5 avg / 16 max
Call network
1414 nodes / 2434 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
62,341
Files
62
Compiled share
93.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
21
Internal functions
23
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.83
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
1 externalGNU make
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-08-12
Latest release
2026-08-12
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 19 (1 internal)includes a package overview page
- Examples that run
- 100%18 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- fraq HTML
- Fix
fraq_concat()discarding output written to a.fifopath when the reader is not keeping up. Buffered bytes are now drained before the writer is closed, matching whatfraq_run()already did.
From NEWS.md in the release
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/traversc/fraq on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Topics
People
- Travers Ching author maintainer copyright holder
-
Facebook, Inc.
copyright holder
Copyright holder of the bundled zstd code
-
Yann Collet
contributor
copyright holder
Author of the bundled zstd library
-
Skibinski Przemyslaw
contributor
copyright holder
Contributor/copyright holder of bundled zstd code
-
Reichardt Tino
contributor
copyright holder
Contributor/copyright holder of bundled zstd code
-
Mori Yuta
contributor
copyright holder
Contributor/copyright holder of bundled zstd code
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("fraq")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.