[med-svn] [Git][med-team/strelka][upstream] New upstream version 2.9.10+dfsg
Andreas Tille
gitlab at salsa.debian.org
Thu May 14 13:58:27 BST 2020
Andreas Tille pushed to branch upstream at Debian Med / strelka
Commits:
2a33aade by Andreas Tille at 2020-05-14T11:45:38+02:00
New upstream version 2.9.10+dfsg
- - - - -
10 changed files:
- − redist/bgzf_extras-v0.1.tar.bz2
- − redist/boost_1_58_0_subset.tar.bz2
- − redist/cmake-2.8.12.tar.bz2
- − redist/cmake-modules-c99fd3/GetGitRevisionDescription.cmake
- − redist/cmake-modules-c99fd3/GetGitRevisionDescription.cmake.in
- − redist/cmake-modules-c99fd3/LICENSE_1_0.txt
- − redist/cmake-modules-c99fd3/README.markdown
- − redist/htslib-1.7-6-g6d2bfb7.tar.bz2
- − redist/pyflow-1.1.20.tar.bz2
- − redist/samtools-1.6.tar.bz2
Changes:
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redist/boost_1_58_0_subset.tar.bz2 deleted
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redist/cmake-2.8.12.tar.bz2 deleted
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=====================================
redist/cmake-modules-c99fd3/GetGitRevisionDescription.cmake deleted
=====================================
@@ -1,128 +0,0 @@
-# - Returns a version string from Git
-#
-# These functions force a re-configure on each git commit so that you can
-# trust the values of the variables in your build system.
-#
-# get_git_head_revision(<refspecvar> <hashvar> [<additional arguments to git describe> ...])
-#
-# Returns the refspec and sha hash of the current head revision
-#
-# git_describe(<var> [<additional arguments to git describe> ...])
-#
-# Returns the results of git describe on the source tree, and adjusting
-# the output so that it tests false if an error occurs.
-#
-# git_get_exact_tag(<var> [<additional arguments to git describe> ...])
-#
-# Returns the results of git describe --exact-match on the source tree,
-# and adjusting the output so that it tests false if there was no exact
-# matching tag.
-#
-# Requires CMake 2.6 or newer (uses the 'function' command)
-#
-# Original Author:
-# 2009-2010 Ryan Pavlik <rpavlik at iastate.edu> <abiryan at ryand.net>
-# http://academic.cleardefinition.com
-# Iowa State University HCI Graduate Program/VRAC
-#
-# Copyright Iowa State University 2009-2010.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-if(__get_git_revision_description)
- return()
-endif()
-set(__get_git_revision_description YES)
-
-# We must run the following at "include" time, not at function call time,
-# to find the path to this module rather than the path to a calling list file
-get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH)
-
-# csaunders: modify to take srcdir as an argument instead of using CMAKE(_CURRENT|)_SOURCE_DIR
-function(get_git_head_revision _refspecvar _hashvar _srcdir)
- set(GIT_PARENT_DIR "${_srcdir}")
- set(GIT_DIR "${GIT_PARENT_DIR}/.git")
- while(NOT EXISTS "${GIT_DIR}") # .git dir not found, search parent directories
- set(GIT_PREVIOUS_PARENT "${GIT_PARENT_DIR}")
- get_filename_component(GIT_PARENT_DIR ${GIT_PARENT_DIR} PATH)
- if(GIT_PARENT_DIR STREQUAL GIT_PREVIOUS_PARENT)
- # We have reached the root directory, we are not in git
- set(${_refspecvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
- set(${_hashvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
- return()
- endif()
- set(GIT_DIR "${GIT_PARENT_DIR}/.git")
- endwhile()
- # check if this is a submodule
- if(NOT IS_DIRECTORY ${GIT_DIR})
- file(READ ${GIT_DIR} submodule)
- string(REGEX REPLACE "gitdir: (.*)\n$" "\\1" GIT_DIR_RELATIVE ${submodule})
- get_filename_component(SUBMODULE_DIR ${GIT_DIR} PATH)
- get_filename_component(GIT_DIR ${SUBMODULE_DIR}/${GIT_DIR_RELATIVE} ABSOLUTE)
- endif()
- set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data")
- if(NOT EXISTS "${GIT_DATA}")
- file(MAKE_DIRECTORY "${GIT_DATA}")
- endif()
-
- if(NOT EXISTS "${GIT_DIR}/HEAD")
- return()
- endif()
- set(HEAD_FILE "${GIT_DATA}/HEAD")
- configure_file("${GIT_DIR}/HEAD" "${HEAD_FILE}" COPYONLY)
-
- configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in"
- "${GIT_DATA}/grabRef.cmake"
- @ONLY)
- include("${GIT_DATA}/grabRef.cmake")
-
- set(${_refspecvar} "${HEAD_REF}" PARENT_SCOPE)
- set(${_hashvar} "${HEAD_HASH}" PARENT_SCOPE)
-endfunction()
-
-# csaunders: modify to take srcdir as an argument instead of using CMAKE(_CURRENT|)_SOURCE_DIR
-function(git_describe _var _srcdir)
- if(NOT GIT_FOUND)
- find_package(Git QUIET)
- endif()
- get_git_head_revision(refspec hash ${_srcdir})
- if(NOT GIT_FOUND)
- set(${_var} "GIT-NOTFOUND" PARENT_SCOPE)
- return()
- endif()
- if(NOT hash)
- set(${_var} "HEAD-HASH-NOTFOUND" PARENT_SCOPE)
- return()
- endif()
-
- # TODO sanitize
- #if((${ARGN}" MATCHES "&&") OR
- # (ARGN MATCHES "||") OR
- # (ARGN MATCHES "\\;"))
- # message("Please report the following error to the project!")
- # message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}")
- #endif()
-
- #message(STATUS "Arguments to execute_process: ${ARGN}")
-
- # csaunders: Modified to leave off explicit ${head} specification so that the --dirty flag
- # can be added in. This probably breaks various submodule/etc, usages, but I can't document which
- execute_process(COMMAND
- "${GIT_EXECUTABLE}" describe ${ARGN}
- WORKING_DIRECTORY ${_srcdir}
- RESULT_VARIABLE res
- OUTPUT_VARIABLE out
- ERROR_QUIET
- OUTPUT_STRIP_TRAILING_WHITESPACE)
- if(NOT res EQUAL 0)
- set(out "${out}-${res}-NOTFOUND")
- endif()
-
- set(${_var} "${out}" PARENT_SCOPE)
-endfunction()
-
-function(git_get_exact_tag _var)
- git_describe(out --exact-match ${ARGN})
- set(${_var} "${out}" PARENT_SCOPE)
-endfunction()
=====================================
redist/cmake-modules-c99fd3/GetGitRevisionDescription.cmake.in deleted
=====================================
@@ -1,38 +0,0 @@
-#
-# Internal file for GetGitRevisionDescription.cmake
-#
-# Requires CMake 2.6 or newer (uses the 'function' command)
-#
-# Original Author:
-# 2009-2010 Ryan Pavlik <rpavlik at iastate.edu> <abiryan at ryand.net>
-# http://academic.cleardefinition.com
-# Iowa State University HCI Graduate Program/VRAC
-#
-# Copyright Iowa State University 2009-2010.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-set(HEAD_HASH)
-
-file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024)
-
-string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS)
-if(HEAD_CONTENTS MATCHES "ref")
- # named branch
- string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}")
- if(EXISTS "@GIT_DIR@/${HEAD_REF}")
- configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY)
- elseif(EXISTS "@GIT_DIR@/logs/${HEAD_REF}")
- configure_file("@GIT_DIR@/logs/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY)
- set(HEAD_HASH "${HEAD_REF}")
- endif()
-else()
- # detached HEAD
- configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY)
-endif()
-
-if(NOT HEAD_HASH)
- file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024)
- string(STRIP "${HEAD_HASH}" HEAD_HASH)
-endif()
=====================================
redist/cmake-modules-c99fd3/LICENSE_1_0.txt deleted
=====================================
@@ -1,23 +0,0 @@
-Boost Software License - Version 1.0 - August 17th, 2003
-
-Permission is hereby granted, free of charge, to any person or organization
-obtaining a copy of the software and accompanying documentation covered by
-this license (the "Software") to use, reproduce, display, distribute,
-execute, and transmit the Software, and to prepare derivative works of the
-Software, and to permit third-parties to whom the Software is furnished to
-do so, all subject to the following:
-
-The copyright notices in the Software and this entire statement, including
-the above license grant, this restriction and the following disclaimer,
-must be included in all copies of the Software, in whole or in part, and
-all derivative works of the Software, unless such copies or derivative
-works are solely in the form of machine-executable object code generated by
-a source language processor.
-
-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, TITLE AND NON-INFRINGEMENT. IN NO EVENT
-SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
-FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
-ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-DEALINGS IN THE SOFTWARE.
=====================================
redist/cmake-modules-c99fd3/README.markdown deleted
=====================================
@@ -1,107 +0,0 @@
-Ryan's CMake Modules
-====================
-
-Ryan A. Pavlik, Ph.D.
-
-<ryan.pavlik at gmail.com> <abiryan at ryand.net>
-<http://academic.cleardefinition.com>
-
-Introduction
-------------
-
-This is a collection of CMake modules that I've produced during the course
-of a variety of software development. There are a number of find modules,
-especially for virtual reality and physical simulation packages, some utility
-modules of more general interest, and some patches or workarounds for
-CMake itself.
-
-Each module is generally documented, and depending on how busy I was
-when I created it, the documentation can be fairly complete.
-
-By now, it also includes contributions both from open-source projects I work on,
-as well as friendly strangers on the Internet contributing their modules. I am
-very grateful for improvements/fixes/pull requests!
-
-How to Integrate
-----------------
-
-These modules are probably best placed wholesale into a `cmake` subdirectory
-of your project source.
-
-If you use Git, try installing [git-subtree][1] (included by default on
-Git for Windows and perhaps for your Linux distro, especially post-1.9.1), so
-you can easily use this repository for subtree merges, updating simply.
-
-For the initial checkout:
-
- cd projectdir
-
- git subtree add --squash --prefix=cmake https://github.com/rpavlik/cmake-modules.git master
-
-For updates:
-
- cd projectdir
-
- git subtree pull --squash --prefix=cmake https://github.com/rpavlik/cmake-modules.git master
-
-If you originally installed this by just copying the files, you'll sadly have
-to delete the directory, commit that, then do the `git subtree add`. Annoying,
-but I don't know a workaround.
-
-If you use some other version control, you can export a copy of this directory
-without the git metadata by calling:
-
- ./export-to-directory.sh yourprojectdir/cmake
-
-You might also consider exporting to a temp directory and merging changes, since
-this will not overwrite by default. You can pass -f to overwrite existing files.
-
-How to Use
-----------
-
-At the minimum, all you have to do is add a line like this near the top
-of your root CMakeLists.txt file (but not before your `project()` call):
-
- list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
-
-You might also want the extra automatic features/fixes included with the
-modules, for that, just add another line following the first one:
-
- include(UseBackportedModules)
-
-Look at `module-help.html`/`.txt` (generated by `update-help.sh` on a unix-like shell with a pre-3.0 version of CMake.)
-either in this directory or online at <http://github.com/rpavlik/cmake-modules/blob/master/module-help.txt>
-for more information on individual modules. Since it requires an older CMake for generation,
-the docs might get out of date, sorry - but you can always look at the files themselves.
-
-
-Licenses
---------
-
-The modules that I wrote myself are all subject to this license:
-
-> Copyright Iowa State University 2009-2014,
-> or Copyright Sensics, Inc. 2014-2015,
-> or Copyright Ryan A. Pavlik 2009-2015
->
-> Distributed under the Boost Software License, Version 1.0.
->
-> (See accompanying file `LICENSE_1_0.txt` or copy at
-> <http://www.boost.org/LICENSE_1_0.txt>)
-
-Modules based on those included with CMake are under the OSI-approved
-BSD license, which is included in each of those modules. A few other modules
-are modified from other sources - when in doubt, look at the `.cmake`.
-
-If you'd like to contribute, that would be great! Just make sure to include
-the license boilerplate in your module, and send a pull request.
-
-Important License Note!
------------------------
-
-If you find this file inside of another project, rather at the top-level
-directory, you're in a separate project that is making use of these modules.
-That separate project can (and probably does) have its own license specifics.
-
-
-[1]: http://github.com/apenwarr/git-subtree "Git Subtree master"
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View it on GitLab: https://salsa.debian.org/med-team/strelka/-/commit/2a33aade59f6a6867883b97a412d7e30337bbe96
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