From 90adf470d2fd327fcae74331edf0ae7a8c96baae Mon Sep 17 00:00:00 2001 From: chaklim Date: Thu, 12 Dec 2019 14:37:18 +0800 Subject: [PATCH 1/5] Fix bug in get_training_array - fix output_labels_from_reference with non-ACGT base --- clair/utils.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/clair/utils.py b/clair/utils.py index f9d84ee..e6560e3 100644 --- a/clair/utils.py +++ b/clair/utils.py @@ -14,7 +14,7 @@ from clair.task.main import output_labels_from_reference, output_labels_from_vcf_columns import shared.param as param from shared.interval_tree import bed_tree_from, is_region_in -from shared.utils import subprocess_popen, IUPAC_base_to_num_dict as BASE2NUM +from shared.utils import subprocess_popen, IUPAC_base_to_num_dict as BASE2NUM, IUPAC_base_to_ACGT_base_dict as BASE2ACGT, BASIC_BASES PREFIX_CHAR_STR = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ" @@ -145,7 +145,7 @@ def get_training_array(tensor_fn, var_fn, bed_fn, shuffle=True, is_allow_duplica if not (is_tree_empty or is_region_in(tree, chrom, int(coord))): continue seq = seq.upper() - if seq[param.flankingBaseNum] not in BASE2NUM: + if seq[param.flankingBaseNum] not in BASIC_BASES: continue key = chrom + ":" + coord @@ -167,7 +167,7 @@ def get_training_array(tensor_fn, var_fn, bed_fn, shuffle=True, is_allow_duplica is_reference = key not in Y if is_reference: - Y[key] = output_labels_from_reference(seq[param.flankingBaseNum]) + Y[key] = output_labels_from_reference(BASE2ACGT[seq[param.flankingBaseNum]]) total += 1 if total % 100000 == 0: From 01accae9cc73780f9c05627fcb632bcba359894c Mon Sep 17 00:00:00 2001 From: chaklim Date: Thu, 12 Dec 2019 16:29:27 +0800 Subject: [PATCH 2/5] Update TRAIN.md --- docs/TRAIN.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/TRAIN.md b/docs/TRAIN.md index d55e88f..3807b2a 100644 --- a/docs/TRAIN.md +++ b/docs/TRAIN.md @@ -236,7 +236,7 @@ parallel --joblog ./tensor2Bin.log -j${THREADS_LOW} \ #### 10. Merge splited binaries into a single binary using the `CombineBins` submodule ```bash -cd ${BINS_FOLDER_PATH} +cd ${DATASET_FOLDER_PATH} python ${CLAIR} CombineBins ``` @@ -441,7 +441,7 @@ parallel --joblog ./tensor2Bin.log -j${THREADS_LOW} "python ${CLAIR} Tensor2Bin #### 9. Merge the splited binaries using the `CombineBins` submodule ```bash -cd ${BINS_FOLDER_PATH} +cd ${DATASET_FOLDER_PATH} python ${CLAIR} CombineBins ``` From 38a9713fbbb33da302ef519e1ae695f42f211497 Mon Sep 17 00:00:00 2001 From: aquaskyline Date: Mon, 16 Dec 2019 15:15:46 +0800 Subject: [PATCH 3/5] switch to bsd 3-clause license --- LICENSE.md | 677 ++--------------------------------------------------- README.md | 2 +- 2 files changed, 27 insertions(+), 652 deletions(-) diff --git a/LICENSE.md b/LICENSE.md index 4ef32f0..486de6e 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,651 +1,26 @@ -GNU Affero General Public License -================================= - -_Version 3, 19 November 2007_ -_Copyright © 2007 Free Software Foundation, Inc. <>_ - -Everyone is permitted to copy and distribute verbatim copies -of this license document, but changing it is not allowed. - -## Preamble - -The GNU Affero General Public License is a free, copyleft license for -software and other kinds of works, specifically designed to ensure -cooperation with the community in the case of network server software. - -The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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Limitation of Liability - -IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING -WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS -THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY -GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE -USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF -DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD -PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), -EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF -SUCH DAMAGES. - -### 17. Interpretation of Sections 15 and 16 - -If the disclaimer of warranty and limitation of liability provided -above cannot be given local legal effect according to their terms, -reviewing courts shall apply local law that most closely approximates -an absolute waiver of all civil liability in connection with the -Program, unless a warranty or assumption of liability accompanies a -copy of the Program in return for a fee. - -_END OF TERMS AND CONDITIONS_ - -## How to Apply These Terms to Your New Programs - -If you develop a new program, and you want it to be of the greatest -possible use to the public, the best way to achieve this is to make it -free software which everyone can redistribute and change under these terms. - -To do so, attach the following notices to the program. It is safest -to attach them to the start of each source file to most effectively -state the exclusion of warranty; and each file should have at least -the “copyright” line and a pointer to where the full notice is found. - - - Copyright (C) - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU Affero General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU Affero General Public License for more details. - - You should have received a copy of the GNU Affero General Public License - along with this program. If not, see . - -Also add information on how to contact you by electronic and paper mail. - -If your software can interact with users remotely through a computer -network, you should also make sure that it provides a way for users to -get its source. For example, if your program is a web application, its -interface could display a “Source” link that leads users to an archive -of the code. There are many ways you could offer source, and different -solutions will be better for different programs; see section 13 for the -specific requirements. - -You should also get your employer (if you work as a programmer) or school, -if any, to sign a “copyright disclaimer” for the program, if necessary. -For more information on this, and how to apply and follow the GNU AGPL, see -<>. +Copyright 2017 Google LLC. + +Redistribution and use in source and binary forms, with or without modification, +are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its contributors + may be used to endorse or promote products derived from this software without + specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/README.md b/README.md index d17244a..baad618 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # Clair - Yet another deep neural network based variant caller -[![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/clair/README.html) +[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/clair/README.html) Contact: Ruibang Luo Email: rbluo@cs.hku.hk From 9e12c65d0c4487c6ef94df7be9724fa88436632e Mon Sep 17 00:00:00 2001 From: aquaskyline Date: Mon, 16 Dec 2019 15:17:07 +0800 Subject: [PATCH 4/5] Revert "switch to bsd 3-clause license" This reverts commit 38a9713fbbb33da302ef519e1ae695f42f211497. --- LICENSE.md | 677 +++++++++++++++++++++++++++++++++++++++++++++++++++-- README.md | 2 +- 2 files changed, 652 insertions(+), 27 deletions(-) diff --git a/LICENSE.md b/LICENSE.md index 486de6e..4ef32f0 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,26 +1,651 @@ -Copyright 2017 Google LLC. - -Redistribution and use in source and binary forms, with or without modification, -are permitted provided that the following conditions are met: - -1. Redistributions of source code must retain the above copyright notice, this - list of conditions and the following disclaimer. - -2. Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimer in the documentation - and/or other materials provided with the distribution. - -3. Neither the name of the copyright holder nor the names of its contributors - may be used to endorse or promote products derived from this software without - specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND -ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +GNU Affero General Public License +================================= + +_Version 3, 19 November 2007_ +_Copyright © 2007 Free Software Foundation, Inc. <>_ + +Everyone is permitted to copy and distribute verbatim copies +of this license document, but changing it is not allowed. + +## Preamble + +The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + +The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Protecting Users' Legal Rights From Anti-Circumvention Law + +No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + +When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such circumvention +is effected by exercising rights under this License with respect to +the covered work, and you disclaim any intention to limit operation or +modification of the work as a means of enforcing, against the work's +users, your or third parties' legal rights to forbid circumvention of +technological measures. + +### 4. 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But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + +The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or updates +for a work that has been modified or installed by the recipient, or for +the User Product in which it has been modified or installed. Access to a +network may be denied when the modification itself materially and +adversely affects the operation of the network or violates the rules and +protocols for communication across the network. + +Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + +### 7. Additional Terms + +“Additional permissions” are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + +When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) 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If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + +If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + +Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; +the above requirements apply either way. + +### 8. Termination + +You may not propagate or modify a covered work except as expressly +provided under this License. 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If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + +### 9. Acceptance Not Required for Having Copies + +You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + +### 10. Automatic Licensing of Downstream Recipients + +Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. 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For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + +### 11. Patents + +A “contributor” is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's “contributor version”. + +A contributor's “essential patent claims” are all patent claims +owned or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, “control” includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + +Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + +In the following three paragraphs, a “patent license” is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To “grant” such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + +If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either **(1)** cause the Corresponding Source to be so +available, or **(2)** arrange to deprive yourself of the benefit of the +patent license for this particular work, or **(3)** arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. “Knowingly relying” means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + +If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + +A patent license is “discriminatory” if it does not include within +the scope of its coverage, prohibits the exercise of, or is +conditioned on the non-exercise of one or more of the rights that are +specifically granted under this License. You may not convey a covered +work if you are a party to an arrangement with a third party that is +in the business of distributing software, under which you make payment +to the third party based on the extent of your activity of conveying +the work, and under which the third party grants, to any of the +parties who would receive the covered work from you, a discriminatory +patent license **(a)** in connection with copies of the covered work +conveyed by you (or copies made from those copies), or **(b)** primarily +for and in connection with specific products or compilations that +contain the covered work, unless you entered into that arrangement, +or that patent license was granted, prior to 28 March 2007. + +Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + +### 12. No Surrender of Others' Freedom + +If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + +### 13. Remote Network Interaction; Use with the GNU General Public License + +Notwithstanding any other provision of this License, if you modify the +Program, your modified version must prominently offer all users +interacting with it remotely through a computer network (if your version +supports such interaction) an opportunity to receive the Corresponding +Source of your version by providing access to the Corresponding Source +from a network server at no charge, through some standard or customary +means of facilitating copying of software. This Corresponding Source +shall include the Corresponding Source for any work covered by version 3 +of the GNU General Public License that is incorporated pursuant to the +following paragraph. + +Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the work with which it is combined will remain governed by version +3 of the GNU General Public License. + +### 14. Revised Versions of this License + +The Free Software Foundation may publish revised and/or new versions of +the GNU Affero General Public License from time to time. Such new versions +will be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + +Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU Affero General +Public License “or any later version” applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU Affero General Public License, you may choose any version ever published +by the Free Software Foundation. + +If the Program specifies that a proxy can decide which future +versions of the GNU Affero General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + +Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + +### 15. Disclaimer of Warranty + +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + +### 16. Limitation of Liability + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + +### 17. Interpretation of Sections 15 and 16 + +If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + +_END OF TERMS AND CONDITIONS_ + +## How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + +To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the “copyright” line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + +If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a “Source” link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + +You should also get your employer (if you work as a programmer) or school, +if any, to sign a “copyright disclaimer” for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +<>. diff --git a/README.md b/README.md index baad618..d17244a 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # Clair - Yet another deep neural network based variant caller -[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/clair/README.html) +[![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/clair/README.html) Contact: Ruibang Luo Email: rbluo@cs.hku.hk From a7fa86deeb9960597f968c3ea7e77acd11e90f3c Mon Sep 17 00:00:00 2001 From: aquaskyline Date: Mon, 16 Dec 2019 15:19:13 +0800 Subject: [PATCH 5/5] switch to bsd 3-clause license --- LICENSE.md | 677 ++--------------------------------------------------- README.md | 2 +- 2 files changed, 27 insertions(+), 652 deletions(-) diff --git a/LICENSE.md b/LICENSE.md index 4ef32f0..0535a94 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,651 +1,26 @@ -GNU Affero General Public License -================================= - -_Version 3, 19 November 2007_ -_Copyright © 2007 Free Software Foundation, Inc. <>_ - -Everyone is permitted to copy and distribute verbatim copies -of this license document, but changing it is not allowed. - -## Preamble - -The GNU Affero General Public License is a free, copyleft license for -software and other kinds of works, specifically designed to ensure -cooperation with the community in the case of network server software. - -The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. By contrast, -our General Public Licenses are intended to guarantee your freedom to -share and change all versions of a program--to make sure it remains free -software for all its users. - -When we speak of free software, we are referring to freedom, not -price. Our General Public Licenses are designed to make sure that you -have the freedom to distribute copies of free software (and charge for -them if you wish), that you receive source code or can get it if you -want it, that you can change the software or use pieces of it in new -free programs, and that you know you can do these things. - -Developers that use our General Public Licenses protect your rights -with two steps: **(1)** assert copyright on the software, and **(2)** offer -you this License which gives you legal permission to copy, distribute -and/or modify the software. - -A secondary benefit of defending all users' freedom is that -improvements made in alternate versions of the program, if they -receive widespread use, become available for other developers to -incorporate. Many developers of free software are heartened and -encouraged by the resulting cooperation. However, in the case of -software used on network servers, this result may fail to come about. -The GNU General Public License permits making a modified version and -letting the public access it on a server without ever releasing its -source code to the public. - -The GNU Affero General Public License is designed specifically to -ensure that, in such cases, the modified source code becomes available -to the community. It requires the operator of a network server to -provide the source code of the modified version running there to the -users of that server. Therefore, public use of a modified version, on -a publicly accessible server, gives the public access to the source -code of the modified version. - -An older license, called the Affero General Public License and -published by Affero, was designed to accomplish similar goals. 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Additional Terms - -“Additional permissions” are terms that supplement the terms of this -License by making exceptions from one or more of its conditions. -Additional permissions that are applicable to the entire Program shall -be treated as though they were included in this License, to the extent -that they are valid under applicable law. If additional permissions -apply only to part of the Program, that part may be used separately -under those permissions, but the entire Program remains governed by -this License without regard to the additional permissions. - -When you convey a copy of a covered work, you may at your option -remove any additional permissions from that copy, or from any part of -it. (Additional permissions may be written to require their own -removal in certain cases when you modify the work.) 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If not, see . - -Also add information on how to contact you by electronic and paper mail. - -If your software can interact with users remotely through a computer -network, you should also make sure that it provides a way for users to -get its source. For example, if your program is a web application, its -interface could display a “Source” link that leads users to an archive -of the code. 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Neither the name of the copyright holder nor the names of its contributors + may be used to endorse or promote products derived from this software without + specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/README.md b/README.md index d17244a..baad618 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # Clair - Yet another deep neural network based variant caller -[![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/clair/README.html) +[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/clair/README.html) Contact: Ruibang Luo Email: rbluo@cs.hku.hk