gbwt 1.6-1

Package Information

Description	Substring index for paths in a graph - shared library Graph BWT is an independent implementation of the graph extension (gPBWT) of the positional Burrows-Wheeler transform (PBWT). Its initial purpose is to embed observed haplotypes in a variation graph. Haplotypes are essentially sequences of nodes in the variation graph, and GBWT is best seen as the multi-string BWT of the node sequences. This package contains the shared library.
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/gbwt.git (browse)
Closes	#1151617
Tracker	https://tracker.debian.org/pkg/gbwt
Uploaded	3 hours ago

New Package Report

.changes◂

Architecture	source amd64
Distribution	unstable
Date	Thu, 22 Oct 2026 11:41:18 +0200
Source	gbwt
Version	1.6-1
Changed-By	Andreas Tille <tille@debian.org>

Changelog◂

gbwt (1.6-1) unstable; urgency=medium
 .
   * Initial release. (Closes: #1151617)

.dsc◂

Package-List	libgbwt-dev deb libdevel optional arch=any libgbwt1 deb libs optional arch=any
Section	libdevel
Priority	optional
Component	main

debian/copyright◂

Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: gbwt
Source: https://github.com/jltsiren/gbwt

Files: *
Copyright: 2017, 2018, Jouni Siren
 2015-2017, Genome Research Ltd.
License: Expat

Files: debian/*
Copyright: 2018 Michael R. Crusoe <michael.crusoe@gmail.com>
           2026 Andreas Tille <tille@debian.org>
License: Expat

License: Expat
 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, 1 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 gbwt version 1.6-1

Summary

Licensing is DFSG-compliant and debian/copyright is accurate: Yes
Packaging is of good quality: Yes
Issues: 0 blocker, 0 important, 1 minor
debian/watch: version 5
debian/copyright: machine-readable
Scan before the review: nothing found

Licensing

The tree is exclusively MIT (Expat) source. debian/copyright is DEP-5 format 1.0 with a single Files: * stanza (Expat) and full licence text; the sole upstream holders it names, Jouni Siren and Genome Research Ltd., match the top-level LICENSE. The pre-review scan found no non-free wording, no built/binary/minified files, and its author check (46 files) confirmed every holder is named. Files that carry no per-file header (e.g. src/support.cpp, src/gbwt.cpp, src/dynamic_gbwt.cpp) are covered by the project LICENSE, so none is unlicensed. Only a copyright-year understatement in debian/copyright is noted (minor).

Packaging

Solid Debian Med packaging: debhelper-compat 14, dh $@ with hardening=+all and build flags passed through, source format 3.0 (quilt), three DEP-3 patches, an autopkgtest, Vcs-*/Homepage, Standards-Version 4.7.4 matching current Policy 4.7.4.1, and correct library/package split (libgbwt1 SONAME .so.1, libgbwt-dev with the sdsl/zstd dev deps). libgbwt-dev depends on libsdsl-dev (>= 2.4), which is only satisfiable by the sdsl 2.4 upload currently in NEW — coordinated, not a fault. d-shlibmove handles installation; the upstream CLI tools are intentionally left unshipped (library-only scope).

Issues

1. [minor] [licensing] debian/copyright understates Jouni Siren's copyright years

Files: debian/copyright:6
Basis: checked, in the package or with a reference tool
Evidence: debian/copyright: Copyright: 2017, 2018, Jouni Siren; LICENSE: Copyright (c) 2017, 2018, ..., 2025, 2026 Jouni Siren.
Problem: The LICENSE enumerates 2017-2026 for Jouni Siren; debian/copyright stops at 2018. Same holder, so not an accuracy blocker, but the file materially understates the copyright span in a machine-readable record.
Fix: Update the Files: * Copyright line to 2017-2026, Jouni Siren (and 2015-2017, Genome Research Ltd.), matching LICENSE.

Verified

Pre-review scan's only finding was the copyright-holder check (46 files); it concluded every holder is named in debian/copyright and flagged no non-free wording, no built/binary/minified files, and no unlicensed terms.
debian/copyright is machine-readable (Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/), with one Files: * stanza (License: Expat, full text included) and a debian/* stanza.
Every file carries the MIT license: src/, include/gbwt/ and tests/ are all Expat; top-level LICENSE is the complete Expat text listing Jouni Siren and Genome Research Ltd.
Full-tree glob (source, tests, include, docs) found only C++ source, headers, Makefiles, textual docs (README.md, SERIALIZATION.md, VERSION2.md) and LICENSE — no binary, minified, font, image, archive or generated files, so no preferred-form-of-modification problem.
debian/copyright Files: * matches all upstream files; no vendor/blob or embedded third-party code (debian ships libsdsl and libzstd separately).
Packaging checked in full: control (Build-Depends: debhelper-compat 14, d-shlibs, libgtest-dev, libsdsl-dev >= 2.4, libzstd-dev, pkgconf; correct binary split, Architecture: any, Sections libs/libdevel), rules (dh $@, hardening=+all, nocheck-guarded tests), three DEP-3 patches, source/format 3.0 (quilt), upstream/metadata, tests/control with smoke autopkgtest.
libgbwt1 package name matches SONAME major 1 (libgbwt.so.1).
Policy version from the policy tool is 4.7.4.1; Standards-Version 4.7.4 is current.
debhelper compat 14 (debhelper-compat (= 14)) so the explicit substvars in control are consistent with dh_gencontrol behavior.
uscan found the packaged version as the newest upstream release (upstream 1.6, packaged 1.6).

Not confirmed

Whether the required libsdsl-dev (>= 2.4) upload now in ftp-master's NEW queue (2.4+dfsg-1) ships the vgteam simple_sds.hpp header that gbwt and the autopkgtest include; the dependency exists in Build-Depends and Depends, so no fault either way.
The build itself could not be run; it was not inspected for a failure since no cause is determinable from the tree.

Proposed changes

None.

Uploader's response to the LLM review

Fix: Update the Files: * Copyright line to 2017-2026, Jouni Siren (and 2015-2017, Genome Research Ltd.), matching LICENSE. --> pushed in Git, will be fixed in next upload.

libsdsl-dev (>= 2.4) is really needed, please make sure it will be accepted first.

— Andreas Tille (tille), 1 hour ago

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