[med-svn] [Git][med-team/bwa-mem2][master] 4 commits: license fixup
Michael R. Crusoe
gitlab at salsa.debian.org
Thu Jul 9 17:53:01 BST 2020
Michael R. Crusoe pushed to branch master at Debian Med / bwa-mem2
Commits:
38b60641 by Michael R. Crusoe at 2020-07-09T17:25:30+02:00
license fixup
- - - - -
cd73bceb by Michael R. Crusoe at 2020-07-09T17:25:30+02:00
simde patch tweak
- - - - -
ca3d3396 by Michael R. Crusoe at 2020-07-09T17:46:11+02:00
build a sse2 version
- - - - -
18d063f7 by Michael R. Crusoe at 2020-07-09T18:45:03+02:00
add docs & manpages
- - - - -
6 changed files:
- debian/control
- debian/copyright
- + debian/docs
- + debian/manpages
- debian/patches/simde
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -6,7 +6,8 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
zlib1g-dev,
- libsimde-dev
+ libsimde-dev,
+ help2man
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/bwa-mem2
Vcs-Git: https://salsa.debian.org/med-team/bwa-mem2.git
=====================================
debian/copyright
=====================================
@@ -44,7 +44,25 @@ License: BSD-2-Clause
Files: debian/*
Copyright: 2019 Dylan Aïssi <daissi at debian.org>
2020 Michael R. Crusoe <crusoe at debian.org>
-License: GPL-3.0+
+License: GPL-3+
+ This program is free software; you can redistribute it and/or modify it under
+ the terms of the GNU 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 General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along with
+ this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL-3'.
+
+Files: debian/patches/*
+Copyright: 2020 Michael R. Crusoe <crusoe at debian.org>
+License: Expat
License: BSD-2-Clause
Redistribution and use in source and binary forms, with or without
@@ -68,3 +86,24 @@ License: BSD-2-Clause
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: 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.
=====================================
debian/docs
=====================================
@@ -0,0 +1,2 @@
+README.md
+NEWS.md
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/patches/simde
=====================================
@@ -1,5 +1,6 @@
From: Michael R. Crusoe <crusoe at debian.org>
Subject: Enable building on non-x86
+
--- bwa-mem2.orig/src/FMI_search.h
+++ bwa-mem2/src/FMI_search.h
@@ -34,7 +34,8 @@
@@ -180,3 +181,40 @@ Subject: Enable building on non-x86
for(i = 0; i <= MAX_SEQ_LEN16; i++) hist[i] = 0;
#else
__m512i zero512 = _mm512_setzero_si512();
+--- bwa-mem2.orig/src/main.cpp
++++ bwa-mem2/src/main.cpp
+@@ -81,10 +81,13 @@
+ #if ((!__AVX512BW__) & (__AVX2__))
+ fprintf(stderr, "Executing in AVX2 mode!!\n");
+ #endif
+-#if ((!__AVX512BW__) && (!__AVX2__) && (__SSE2__))
++#if ((!__AVX512BW__) && (!__AVX2__) && (__SSE4_1__))
+ fprintf(stderr, "Executing in SSE4.1 mode!!\n");
+ #endif
+-#if ((!__AVX512BW__) && (!__AVX2__) && (!__SSE2__))
++#if ((!__AVX512BW__) && (!__AVX2__) && (!__SSE4_1__) && (__SSE2__))
++ fprintf(stderr, "Executing in SSE2 mode!!\n");
++#endif
++#if ((!__AVX512BW__) && (!__AVX2__) && (!__SSE4_1__) && (!__SSE2__))
+ fprintf(stderr, "Executing in Scalar mode!!\n");
+ #endif
+ fprintf(stderr, "-----------------------------\n");
+--- bwa-mem2.orig/src/bandedSWA.cpp
++++ bwa-mem2/src/bandedSWA.cpp
+@@ -4120,16 +4120,6 @@
+ return;
+ }
+
+-/********************************************************************************/
+-/* SSE2 - 8 bit version */
+-#ifndef __SSE4_1__
+-static inline __m128i _mm_blendv_epi8 (__m128i x, __m128i y, __m128i mask)
+-{
+- // Replace bit in x with bit in y when matching bit in mask is set:
+- return _mm_or_si128(_mm_andnot_si128(mask, x), _mm_and_si128(mask, y));
+-}
+-#endif
+-
+ #define ZSCORE8(i4_128, y4_128) \
+ { \
+ __m128i tmpi = _mm_sub_epi8(i4_128, x128); \
=====================================
debian/rules
=====================================
@@ -1,5 +1,7 @@
#!/usr/bin/make -f
+SHELL=bash # needed for the <(echo …) process subsitution temporary file
+include /usr/share/dpkg/default.mk
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
ifeq (,$(filter $(DEB_HOST_ARCH),amd64 i386))
@@ -12,10 +14,18 @@ endif
override_dh_auto_build:
ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))
+ dh_auto_build -- EXE=bwa-mem2.sse2 ARCH_FLAGS='-msse2'
dh_auto_build -- multi
else
dh_auto_build -- ARCH_FLAGS=' '
endif
+ help2man --no-discard-stderr --version-string="$(DEB_VERSION_UPSTREAM)" \
+ --help-option=' ' --no-info ./bwa-mem2 --name="Sequence alignment using Burrows-Wheeler Transform" \
+ > debian/bwa-mem2.1
+ help2man --no-discard-stderr --version-string="$(DEB_VERSION_UPSTREAM)" \
+ --help-option=' ' --no-info './bwa-mem2 mem' \
+ --include <(echo -e "[NAME]\nbwa-mem2_mem \- Sequence alignment using Burrows-Wheeler Transform") \
+ > debian/bwa-mem2-mem.1
# ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
# dh_auto_build --sourcedir=test -- CXX=g++
View it on GitLab: https://salsa.debian.org/med-team/bwa-mem2/-/compare/466c9ca17158e513a8419062706b83ef9bf768fe...18d063f78d51b58c00b69aa2cc5ca8d94abc3abc
--
View it on GitLab: https://salsa.debian.org/med-team/bwa-mem2/-/compare/466c9ca17158e513a8419062706b83ef9bf768fe...18d063f78d51b58c00b69aa2cc5ca8d94abc3abc
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