gsim is distributed under the GNU General Public License version 3 (GPL-3).
Founder-model provenance
------------------------
The gsim founder model is a clean native C++ implementation informed by the
scientific model and behavior of HAPNEST. No HAPNEST source code is included.
The reference source was inspected at the pinned revision:
https://github.com/intervene-EU-H2020/synthetic_data/tree/ba52da1a63cf609306ea92540b3d130fa1efd213
The corresponding paper is Wharrie et al. (2023), "HAPNEST: efficient,
large-scale generation and evaluation of synthetic datasets for human
genetics", Bioinformatics 39, btad535:
https://doi.org/10.1093/bioinformatics/btad535
HAPNEST is distributed under GPL-3; its license at the pinned revision is:
https://github.com/intervene-EU-H2020/synthetic_data/blob/ba52da1a63cf609306ea92540b3d130fa1efd213/LICENSE
gbits provenance and MIT notice
-------------------------------
Internalized packed-haplotype, HAP v1, and BED components originated in our
gbits project at revision 089bf1e69dea356248a62bb2d3bded4e84c64f7f. The
adapted components retain the following applicable MIT notice. Checked BED
record I/O and the scalar selected-marker/all-trait multiplication loop in
src/bed_reader.{h,cpp} additionally adapt gbits/src/bed_reader.cpp at revision
02298cbb30e5d88acc0759d608631a0559675840 (xmat_scalar). No gbits adapter,
shared-library interface, scheduling framework, or gmat wrapper is included:
MIT License
Copyright (c) 2026 gbits contributors
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.
gmat provenance
---------------
Internalized variant/sample metadata, BIM/FAM, and strict phased-VCF
components originated in our own gmat project at revision
33d6751abf00c41a15223459df7cae028d54b4b5. They are distributed as part of
gsim under gsim's GPL-3 license.
Authoritative
source