MERGE / merge-cli — licence
===========================

This project is split into two parts with different terms, because one of them
we can give away freely and the other we cannot.

  1. The SOFTWARE, and the four MERGE ensemble models
     (merge_cli/data/models/MERGE_noAlphaGenome_{coding,splicing,noncoding,
     nonsnv}.pkl), are under the MIT licence, reproduced in full below.
     No field-of-use restriction: commercial use, redistribution and
     modification are all permitted.

     The ensembles were previously CC BY-NC 4.0, because every one of their
     feature panels included an AlphaGenome-derived feature. They are now
     trained on a candidate pool with every alphagenome_* column removed, so no
     AlphaGenome output went into them and that restriction no longer applies.

  2. The AlphaGenome percentile table
     (merge_cli/data/models/alphagenome_reference_quantiles.json)
     is under Creative Commons
     Attribution-NonCommercial 4.0 International (CC BY-NC 4.0):
     https://creativecommons.org/licenses/by-nc/4.0/

     It pairs every distinct AlphaGenome score observed in the MERGE benchmark
     with its mid-rank percentile. No label and no fitted parameter is involved,
     so it is not a model trained on AlphaGenome output. The table is still a
     derivative of AlphaGenome output, and AlphaGenome's API is offered for
     non-commercial use only, so we license it conservatively rather than claim
     a permissiveness we are not in a position to grant.

     It is used only for the optional MERGE + AlphaGenome average, offered on
     splicing and non-coding variants. Delete it and MERGE still runs: the
     ensembles score as normal for all four variant classes and the average is
     reported as unavailable. For commercial use, that is the supported
     configuration.

Third-party models, databases and services that MERGE calls are covered by
neither of the above. See THIRD_PARTY_NOTICES.md for each one's licence, the
four that restrict commercial use, and the attributions they require. MERGE
redistributes none of them.


NOT FOR CLINICAL USE
--------------------

Independently of any licence term: MERGE is a research prototype. It is not a
medical device, has not been clinically validated, and has no regulatory
approval or clearance in any jurisdiction. Its output must not be used for
diagnosis, prognosis, treatment decisions, genetic counselling, or any other
clinical or patient-facing purpose. Variant interpretation remains the
responsibility of qualified professionals following established guidelines such
as ACMG/AMP.


CITATION
--------

Not a licence condition, but if MERGE contributes to work you publish, please
cite the MERGE paper and the web server (https://merge.fanglab.cn), and cite the
upstream models whose scores you used — the citations are listed in
THIRD_PARTY_NOTICES.md.


MIT License
-----------

Copyright (c) 2026 The MERGE Project Team
Zhongshan School of Medicine, Sun Yat-sen University

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.

Contact: chenyanggza01@163.com / fangli9@mail.sysu.edu.cn
