gfaz 0.0~git20260915.f1c1b7f-1
Package Information
| Description | GFA compression tool based on 2-mer reordering GFAz compresses Graphical Fragment Assembly (GFA) files by reordering segments and encoding paths with a learned grammar on top of Zstandard. In the upstream benchmarks it reaches up to 20x higher compression ratio than gzip and 13x higher than Zstandard. Besides compression, the tool computes pangenome statistics (growth curves, PAV, similarity, depth, deconstruction) directly on the compressed container without decompressing to GFA. This package contains the gfaz command line tool. |
|---|---|
| Maintainer | Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> |
| Changed By | Andreas Tille <tille@debian.org> |
| Sponsor | tille@debian.org |
| Distribution | unstable |
| Architecture | any |
| VCS | git: https://salsa.debian.org/med-team/gfaz.git (browse) |
| Closes | #1151944 |
| Tracker | https://tracker.debian.org/pkg/gfaz |
| Uploaded | 2 hours ago |
New Package Report
.changes
| Distribution | unstable |
|---|---|
| Date | Sun, 25 Oct 2026 16:57:11 +0100 |
| Source | gfaz |
| Version | 0.0~git20260915.f1c1b7f-1 |
| Changed-By | Andreas Tille <tille@debian.org> |
| Architecture | source amd64 |
Changelog
gfaz (0.0~git20260915.f1c1b7f-1) unstable; urgency=medium . * Initial release. (Closes: #1151944)
.dsc
| Section | science |
|---|---|
| Priority | optional |
| Component | main |
| Package-List | gfaz deb science optional arch=any python3-gfaz deb python optional arch=any |
debian/copyright
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: GFAz Source: https://github.com/babyplutokurt/GFAz Files: * Copyright: 2026 The GFAz authors (see LICENSE) License: MIT Files: extern/robin_hood/* Copyright: 2018-2021 Martin Ankerl License: MIT Files: debian/* Copyright: 2026 Andreas Tille <tille@debian.org> License: MIT License: MIT Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
DFSG Assistant LLM REVIEW 0 blocker, 0 important, 0 minor
This is an LLM based review using a Debian Inference based workflow. It was not written by a member of the DFSG team and has not been checked by one. It is not a decision on the package: it may be wrong, and it may have missed things.
Reviewed 1 hour ago.
Report
DFSG NEW review for gfaz version 0.0~git20260915.f1c1b7f-1
Summary
- Licensing is DFSG-compliant and
debian/copyrightis accurate: Yes - Packaging is of good quality: Yes
- Issues: 0 blocker, 0 important, 0 minor
- debian/watch: version 5
- debian/copyright: machine-readable
- Scan before the review: nothing found
Licensing
debian/copyright is machine-readable DEP-5 and accurately covers the whole tree. All upstream source, documentation, scripts, test fixtures and example.gfa are MIT ("2026 The GFAz authors"), matching the root LICENSE. The only vendored third-party code actually shipped is extern/robin_hood/robin_hood.h (MIT, Martin Ankerl 2018-2021), which has its own correct stanza. The other extern/ submodule directories (cuCollections, fse, pybind11, zstd) are empty in the tarball, so nothing else needs licensing. There are no non-free terms, no files without a licence, no built/binary files lacking source, and no undisclosed copyright holders.
Packaging
The packaging is clean and follows current practice: debhelper compat 14 with the cmake buildsystem, dh-sequence-python3 for the Python extension, a single DEP-3 patch that switches the empty pybind11 submodule to find_package, a hermetic autopkgtest exercising both the CLI and the Python module, and a correct two-binary-package split (gfaz CLI, python3-gfaz extension). Standards-Version 4.7.4 is current (Policy is 4.7.4.1). No policy violations, missing dependencies, or upgrade hazards were found.
Issues
None.
Verified
- Prescan author check: no copyright holder is missing from debian/copyright (its own result: every holder found is named); no file was flagged for individual attention.
- extern/cuCollections, extern/fse, extern/pybind11 and extern/zstd are empty directories (git submodules whose contents are not shipped in the tarball), so they contain no files requiring a stanza.
- extern/robin_hood/robin_hood.h is the only vendored third-party file; its embedded header states SPDX-License-Identifier: MIT and Copyright (c) 2018-2021 Martin Ankerl, matching the extern/robin_hood/* stanza.
- There is no COPYING, NOTICE or AUTHORS file anywhere in the tree besides the root LICENSE; the only copyright/licence wording outside debian/ and LICENSE is the MIT header inside robin_hood.h.
- example.gfa and tests/fixtures/*.gfa / *.bed / *.golden are GFA test/example data with no independent authorship, covered by the Files: * MIT stanza.
- No compiled, minified, archived or otherwise non-preferred-form files exist in the tree; the source is all C++/CUDA/Python/Markdown/CMake text.
- dh-sequence-python3 is a virtual package provided by dh-python 7.20261019, so the Build-Depends is valid.
- uscan found the packaged version as the newest upstream release (upstream
0.0~git20260915.f1c1b7f, packaged0.0~git20260915.f1c1b7f).
Not confirmed
- Why the model asked for what a review has no use for. During this review it asked once for something outside the package and the reviewing system (another file of the sandbox, or a URL), or was given part of the review tooling's own configuration, and that was refused or withheld. A model does this when something it has read tells it to, so look in the package for text addressed to a reviewing program, and treat this report with suspicion. Refused:
read: "/home/review" is not a file of the package or of the reviewing system.
Proposed changes
None.
Uploader's response to the LLM review
The uploader was emailed about the review 1 hour ago.