Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: StringTie
Source: https://github.com/gpertea/stringtie
Files-Excluded:
 samtools-0.1.18
 SuperReads_RNA
#gclib # Upstream does not want this to be distributed system-wide

Files: *
Copyright: 2019 Mihaela Pertea, Geo Pertea
License: Expat

Files: gclib/GBitVec.h
Copyright: 2019 Mihaela Pertea, Geo Pertea
                this code is lifted from LLVM (llvm.org, BitVector.h)
License: Apache-2.0 with LLVM-exception

Files: gclib/GThreads.cpp gclib/GThreads.h
Copyright: 2010 Marcus Geelnard
           (with minor modifications by Geo Pertea)
License: custom
 This software is provided 'as-is', without any express or implied
 warranty. In no event will the authors be held liable for any damages
 arising from the use of this software.
 .
 Permission is granted to anyone to use this software for any purpose,
 including commercial applications, and to alter it and redistribute it
 freely, subject to the following restrictions:
 .
  1. The origin of this software must not be misrepresented; you must not
     claim that you wrote the original software. If you use this software
     in a product, an acknowledgment in the product documentation would be
     appreciated but is not required.
 .
  2. Altered source versions must be plainly marked as such, and must not be
     misrepresented as being the original software.
 .
  3. This notice may not be removed or altered from any source
     distribution.

Files: debian/*
Copyright: 2019 Steffen Moeller <moeller@debian.org>
License: Artistic-2.0

License: Artistic-2.0
 .
 Preamble
 .
 This license establishes the terms under which a given free software
 Package may be copied, modified, distributed, and/or redistributed. The
 intent is that the Copyright Holder maintains some artistic control over
 the development of that Package while still keeping the Package
 available as open source and free software.
 .
 You are always permitted to make arrangements wholly outside of this
 license directly with the Copyright Holder of a given Package. If the
 terms of this license do not permit the full use that you propose to
 make of the Package, you should contact the Copyright Holder and seek a
 different licensing arrangement. Definitions
 .
 "Copyright Holder" means the individual(s) or organization(s) named in
 the copyright notice for the entire Package.
 .
 "Contributor" means any party that has contributed code or other
 material to the Package, in accordance with the Copyright Holder's
 procedures.
 .
 "You" and "your" means any person who would like to copy, distribute, or
 modify the Package.
 .
 "Package" means the collection of files distributed by the Copyright
 Holder, and derivatives of that collection and/or of those files. A
 given Package may consist of either the Standard Version, or a Modified
 Version.
 .
 "Distribute" means providing a copy of the Package or making it
 accessible to anyone else, or in the case of a company or organization,
 to others outside of your company or organization.
 .
 "Distributor Fee" means any fee that you charge for Distributing this
 Package or providing support for this Package to another party. It does
 not mean licensing fees.
 .
 "Standard Version" refers to the Package if it has not been modified, or
 has been modified only in ways explicitly requested by the Copyright
 Holder.
 .
 "Modified Version" means the Package, if it has been changed, and such
 changes were not explicitly requested by the Copyright Holder.
 .
 "Original License" means this Artistic License as Distributed with the
 Standard Version of the Package, in its current version or as it may be
 modified by The Perl Foundation in the future.
 .
 "Source" form means the source code, documentation source, and
 configuration files for the Package.
 .
 "Compiled" form means the compiled bytecode, object code, binary, or any
 other form resulting from mechanical transformation or translation of
 the Source form. Permission for Use and Modification Without
 Distribution
 .
 (1) You are permitted to use the Standard Version and create and use
 Modified Versions for any purpose without restriction, provided that you
 do not Distribute the Modified Version. Permissions for Redistribution
 of the Standard Version
 .
 (2) You may Distribute verbatim copies of the Source form of the
 Standard Version of this Package in any medium without restriction,
 either gratis or for a Distributor Fee, provided that you duplicate all
 of the original copyright notices and associated disclaimers. At your
 discretion, such verbatim copies may or may not include a Compiled form
 of the Package.
 .
 (3) You may apply any bug fixes, portability changes, and other
 modifications made available from the Copyright Holder. The resulting
 Package will still be considered the Standard Version, and as such will
 be subject to the Original License. Distribution of Modified Versions of
 the Package as Source
 .
 (4) You may Distribute your Modified Version as Source (either gratis or
 for a Distributor Fee, and with or without a Compiled form of the
 Modified Version) provided that you clearly document how it differs from
 the Standard Version, including, but not limited to, documenting any
 non-standard features, executables, or modules, and provided that you do
 at least ONE of the following:
 .
 (a) make the Modified Version available to the Copyright Holder of the
 Standard Version, under the Original License, so that the Copyright
 Holder may include your modifications in the Standard Version. (b)
 ensure that installation of your Modified Version does not prevent the
 user installing or running the Standard Version. In addition, the
 Modified Version must bear a name that is different from the name of the
 Standard Version. (c) allow anyone who receives a copy of the Modified
 Version to make the Source form of the Modified Version available to
 others under (i) the Original License or (ii) a license that permits the
 licensee to freely copy, modify and redistribute the Modified Version
 using the same licensing terms that apply to the copy that the licensee
 received, and requires that the Source form of the Modified Version, and
 of any works derived from it, be made freely available in that license
 fees are prohibited but Distributor Fees are allowed. Distribution of
 Compiled Forms of the Standard Version or Modified Versions without the
 Source
 .
 (5) You may Distribute Compiled forms of the Standard Version without
 the Source, provided that you include complete instructions on how to
 get the Source of the Standard Version. Such instructions must be valid
 at the time of your distribution. If these instructions, at any time
 while you are carrying out such distribution, become invalid, you must
 provide new instructions on demand or cease further distribution. If you
 provide valid instructions or cease distribution within thirty days
 after you become aware that the instructions are invalid, then you do
 not forfeit any of your rights under this license.
 .
 (6) You may Distribute a Modified Version in Compiled form without the
 Source, provided that you comply with Section 4 with respect to the
 Source of the Modified Version. Aggregating or Linking the Package
 .
 (7) You may aggregate the Package (either the Standard Version or
 Modified Version) with other packages and Distribute the resulting
 aggregation provided that you do not charge a licensing fee for the
 Package. Distributor Fees are permitted, and licensing fees for other
 components in the aggregation are permitted. The terms of this license
 apply to the use and Distribution of the Standard or Modified Versions
 as included in the aggregation.
 .
 (8) You are permitted to link Modified and Standard Versions with other
 works, to embed the Package in a larger work of your own, or to build
 stand-alone binary or bytecode versions of applications that include the
 Package, and Distribute the result without restriction, provided the
 result does not expose a direct interface to the Package. Items That are
 Not Considered Part of a Modified Version
 .
 (9) Works (including, but not limited to, modules and scripts) that
 merely extend or make use of the Package, do not, by themselves, cause
 the Package to be a Modified Version. In addition, such works are not
 considered parts of the Package itself, and are not subject to the terms
 of this license. General Provisions
 .
 (10) Any use, modification, and distribution of the Standard or Modified
 Versions is governed by this Artistic License. By using, modifying or
 distributing the Package, you accept this license. Do not use, modify,
 or distribute the Package, if you do not accept this license.
 .
 (11) If your Modified Version has been derived from a Modified Version
 made by someone other than you, you are nevertheless required to ensure
 that your Modified Version complies with the requirements of this
 license.
 .
 (12) This license does not grant you the right to use any trademark,
 service mark, tradename, or logo of the Copyright Holder.
 .
 (13) This license includes the non-exclusive, worldwide, free-of-charge
 patent license to make, have made, use, offer to sell, sell, import and
 otherwise transfer the Package with respect to any patent claims
 licensable by the Copyright Holder that are necessarily infringed by the
 Package. If you institute patent litigation (including a cross-claim or
 counterclaim) against any party alleging that the Package constitutes
 direct or contributory patent infringement, then this Artistic License
 to you shall terminate on the date that such litigation is filed.
 .
 (14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT
 HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED
 WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
 PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT
 PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER
 OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR
 CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE,
 EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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.

License: Apache-2.0 with LLVM-exception
 .
 The Apache license is found in /usr/share/common-licenses/Apache-2.0 on Debian
 systems. The following exception applies:
 .
 --- LLVM Exceptions to the Apache 2.0 License ----
 .
 As an exception, if, as a result of your compiling your source code, portions
 of this Software are embedded into an Object form of such source code, you
 may redistribute such embedded portions in such Object form without complying
 with the conditions of Sections 4(a), 4(b) and 4(d) of the License.
 .
 In addition, if you combine or link compiled forms of this Software with
 software that is licensed under the GPLv2 ("Combined Software") and if a
 court of competent jurisdiction determines that the patent provision (Section
 3), the indemnity provision (Section 9) or other Section of the License
 conflicts with the conditions of the GPLv2, you may retroactively and
 prospectively choose to deem waived or otherwise exclude such Section(s) of
 the License, but only in their entirety and only with respect to the Combined
 Software.

