--- /dev/null
--- /dev/null
++pbbam (0.7.4+ds-1) unstable; urgency=medium
++
++ * New upstream release snapshot
++ - Exclude dependency convenience copy
++ - Update patches
++ - Update running of tests at build-time
++ - Update .install files
++ - Update autopkgtest commands
++ * Use debhelper compat 10
++ * libpbbam-dev: depend on libssl-dev
++
++ -- Afif Elghraoui <afif@debian.org> Sat, 21 Jan 2017 23:48:21 -0800
++
++pbbam (0.7.0-1) unstable; urgency=medium
++
++ * Imported Upstream version 0.7.0
++ * Update patches
++
++ -- Afif Elghraoui <afif@debian.org> Sun, 30 Oct 2016 14:31:49 -0700
++
++pbbam (0.5.0-3) unstable; urgency=low
++
++ * Fix cmake arguments to properly position LDFLAGS for -Wl,--as-needed.
++ Thanks to Steve Langasek (Closes: #841671)
++
++ -- Afif Elghraoui <afif@debian.org> Sun, 23 Oct 2016 14:07:27 -0700
++
++pbbam (0.5.0-2) unstable; urgency=low
++
++ * libpbbam-dev: add dependency on libhts-dev
++
++ -- Afif Elghraoui <afif@debian.org> Sun, 17 Jul 2016 23:29:34 -0700
++
++pbbam (0.5.0-1) unstable; urgency=medium
++
++ * New upstream revision (git 79ab246 from 2016-02-23)
++ * Declare additional copyrights to avoid repacking tarball
++ * Update patches
++ * Update Standards-Version to 3.9.8
++ * Use encrypted protocols for VCS URLs
++ * Clean up d/control and d/rules
++ * Use dh-exec for library installation rather than sed-within-d/rules
++ * Set up build-time tests for command-line tools
++ * Add binary package for command-line tools
++ * Install library to main library path
++ * Configure autopkgtests
++ * Use documentation page as Homepage
++ * Remove build-dependency on doxygen
++ * Add TODO list
++
++ -- Afif Elghraoui <afif@debian.org> Tue, 05 Jul 2016 03:25:49 -0700
++
++pbbam (0.1.0~20150813+git4e9e417+dfsg-1) unstable; urgency=low
++
++ * Initial release (Closes: #798220)
++
++ -- Afif Elghraoui <afif@ghraoui.name> Fri, 18 Sep 2015 02:40:24 -0700
--- /dev/null
--- /dev/null
++Source: pbbam
++Section: libs
++Priority: optional
++Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
++Uploaders: Afif Elghraoui <afif@debian.org>
++Build-Depends:
++ debhelper (>= 10),
++ dh-exec,
++ cmake,
++ python,
++# swig3.0,
++ libboost-dev (>= 1.54),
++ zlib1g-dev,
++ libssl-dev,
++ libhts-dev,
++# Test-Depends:
++# libgtest-dev,
++ python-cram,
++ samtools,
++Standards-Version: 3.9.8
++Homepage: http://pbbam.readthedocs.org/en/latest/index.html
++Vcs-Git: https://anonscm.debian.org/git/debian-med/pbbam.git
++Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pbbam.git
++
++Package: pbbamtools
++Section: science
++Architecture: any
++Depends:
++ ${shlibs:Depends},
++ ${misc:Depends},
++ libpbbam (= ${binary:Version}),
++Recommends: samtools
++Description: processing Pacific Biosciences binary alignment/map files
++ The BAM format is a binary, compressed, record-oriented container format
++ for raw or aligned sequence reads. The associated SAM format is a text
++ representation of the same data. The specifications for BAM/SAM are maintained
++ by the SAM/BAM Format Specification Working Group.
++ .
++ PacBio-produced BAM files are fully compatible with the BAM specification,
++ but makes use of the extensibility mechanisms of the BAM specification to
++ encode PacBio-specific information.
++ .
++ This package provides command-line utilities for working with PacBio BAM
++ files.
++
++Package: libpbbam
++Architecture: any
++Multi-Arch: same
++Pre-Depends:
++ ${misc:Pre-Depends}
++Depends:
++ ${shlibs:Depends},
++ ${misc:Depends},
++Description: Pacific Biosciences binary alignment/map (BAM) library
++ The BAM format is a binary, compressed, record-oriented container format
++ for raw or aligned sequence reads. The associated SAM format is a text
++ representation of the same data. The specifications for BAM/SAM are maintained
++ by the SAM/BAM Format Specification Working Group.
++ .
++ PacBio-produced BAM files are fully compatible with the BAM specification,
++ but makes use of the extensibility mechanisms of the BAM specification to
++ encode PacBio-specific information. The pbbam library provides tools to
++ work with these files
++
++Package: libpbbam-dev
++Section: libdevel
++Architecture: any
++Depends:
++ libpbbam (= ${binary:Version}),
++ libhts-dev,
++ libssl-dev,
++ ${misc:Depends},
++Description: Pacific Biosciences binary alignment/map (BAM) library (headers)
++ The BAM format is a binary, compressed, record-oriented container format
++ for raw or aligned sequence reads. The associated SAM format is a text
++ representation of the same data. The specifications for BAM/SAM are maintained
++ by the SAM/BAM Format Specification Working Group.
++ .
++ PacBio-produced BAM files are fully compatible with the BAM specification,
++ but makes use of the extensibility mechanisms of the BAM specification to
++ encode PacBio-specific information. The pbbam library provides tools to
++ work with these files
++ .
++ This package contains the library header files.
--- /dev/null
--- /dev/null
++Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
++Upstream-Name: pbbam
++Upstream-Contact: Pacific Biosciences <devnet@pacificbiosciences.com>
++Source: https://github.com/PacificBiosciences/pbbam
++Files-Excluded: third-party
++
++Files: *
++Copyright: 2014-2016 Pacific Biosciences of California, Inc. <devnet@pacificbiosciences.com>
++License: PacBio-BSD-3-Clause
++
++Files: cmake/FindCSharp.cmake
++ cmake/FindMono.cmake
++ cmake/UseCSharp.cmake
++ cmake/UseDotNetFrameworkSdk.cmake
++ cmake/UseMono.cmake
++Copyright: 2006-2010 Mathieu Malaterre <mathieu.malaterre@gmail.com>
++Comment: These files are from GDCM (as indicated in the file headers).
++ The license terms have been retrieved from there.
++License: MM-BSD-3-Clause
++
++Files: src/pugixml/*
++Copyright: 2006-2014 Arseny Kapoulkine <arseny.kapoulkine@gmail.com>
++ 2003 Kristen Wegner <kristen@tima.net>
++License: MIT
++
++Files: tools/common/OptionParser.*
++Copyright: 2010 Johannes Weißl <jargon@molb.org>
++License: BSD-3-Clause or BSD-2-Clause
++
++Files: debian/*
++Copyright: 2015-2016 Afif Elghraoui <afif@debian.org>
++License: PacBio-BSD-3-Clause
++
++License: PacBio-BSD-3-Clause
++ Redistribution and use in source and binary forms, with or without
++ modification, are permitted (subject to the limitations in the
++ disclaimer below) 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 Pacific Biosciences nor the names of its
++ contributors may be used to endorse or promote products derived
++ from this software without specific prior written permission.
++ .
++ NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
++ GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
++ BIOSCIENCES AND ITS 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 PACIFIC BIOSCIENCES OR ITS
++ 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.
++
++License: MM-BSD-3-clause
++ 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 name of Mathieu Malaterre, or CREATIS, nor the names of any
++ contributors (CNRS, INSERM, UCB, Universite Lyon I), 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 AUTHORS 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.
++
++License: BSD-3-Clause
++ 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 University 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 HOLDERS 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.
++
++License: BSD-2-Clause
++ 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.
++ .
++ 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.
++
++License: MIT
++ 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.
projects / pbbam.git / commitdiff