New Upstream Snapshot - spoa
Ready changes
Summary
Merged new upstream version: 4.0.8+git20210712.1.981ad59 (was: 4.0.8).
Resulting package
Built on 2023-01-17T00:29 (took 3m32s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-snapshots libspoa-devapt install -t fresh-snapshots libspoa7.0.0-dbgsymapt install -t fresh-snapshots libspoa7.0.0apt install -t fresh-snapshots spoa-dbgsymapt install -t fresh-snapshots spoa
Lintian Result
- libspoa-dev_4.0.8+git20210712.1.981ad59-1~jan+nus1_amd64.deb
- libspoa7.0.0-dbgsym_4.0.8+git20210712.1.981ad59-1~jan+nus1_amd64.deb
- libspoa7.0.0_4.0.8+git20210712.1.981ad59-1~jan+nus1_amd64.deb
- spoa-dbgsym_4.0.8+git20210712.1.981ad59-1~jan+nus1_amd64.deb
- spoa_4.0.8+git20210712.1.981ad59-1~jan+nus1.dsc
- spoa_4.0.8+git20210712.1.981ad59-1~jan+nus1_amd64.buildinfo
- spoa_4.0.8+git20210712.1.981ad59-1~jan+nus1_amd64.deb
- spoa_4.0.8+git20210712.1.981ad59-1~jan+nus1_amd64.changes
Diff
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 56ccb7b..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-# Compiled Object files
-build/
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 707f717..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-language: cpp
-
-matrix:
- include:
- - name: "GCC 4.8 (Linux)" # GCC 4.8.5 & CMake 3.12.4
- os: linux
- dist: xenial
- addons:
- apt:
- sources:
- - ubuntu-toolchain-r-test
- packages:
- - g++-4.8
- env:
- - SET_COMPILER="export CC=gcc-4.8 && export CXX=g++-4.8"
-
- - name: "Clang 3.5 (Linux)" # Clang 3.5.0 & CMake 3.12.4
- os: linux
- dist: xenial
- addons:
- apt:
- packages:
- - clang-3.5
- env:
- - SET_COMPILER="export CC=clang-3.5 && export CXX=clang++-3.5"
-
- - name: "Clang Xcode 9.4 (OSX)" # Clang 9.4.1 & CMake 3.15.5
- os: osx
- osx_image: xcode9.4
-
-before_install:
- - eval "${SET_COMPILER}"
-
-install:
- - mkdir build && cd build
- - cmake -DCMAKE_BUILD_TYPE=Release .. && make
-
-script:
- - ./bin/spoa --version
- - ./bin/spoa_test
-
-notifications:
- email:
- on_failure: always
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 883b3bf..2cb3b82 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,6 +1,6 @@
cmake_minimum_required(VERSION 3.12)
-project(spoa VERSION 4.0.8
+project(spoa VERSION 4.0.9
LANGUAGES CXX
DESCRIPTION "Spoa is a c++ library (and tool) for SIMD vectorized partial order alignment.")
diff --git a/README.md b/README.md
index 798d155..30a0f00 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
# Spoa
[](https://github.com/rvaser/spoa/releases/latest)
-[](https://travis-ci.com/rvaser/spoa)
+
[](https://doi.org/10.1101/gr.214270.116)
Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences (as described in 10.1093/bioinformatics/btg109). It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap), and three gap modes: linear, affine and convex (piecewise affine). It also supports Intel SSE4.1+ and AVX2 vectorization (marginally faster due to high latency shifts), [SIMDe](https://github.com/simd-everywhere/simde) and dispatching.
diff --git a/debian/changelog b/debian/changelog
index da613b0..b4fdc50 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+spoa (4.0.8+git20210712.1.981ad59-1) UNRELEASED; urgency=low
+
+ * New upstream snapshot.
+
+ -- Debian Janitor <janitor@jelmer.uk> Tue, 17 Jan 2023 00:27:03 -0000
+
spoa (4.0.8-1) unstable; urgency=medium
* Fix watch file
diff --git a/debian/patches/fix-ftbfs-gcc-10.patch b/debian/patches/fix-ftbfs-gcc-10.patch
index 5fe114f..5d09855 100644
--- a/debian/patches/fix-ftbfs-gcc-10.patch
+++ b/debian/patches/fix-ftbfs-gcc-10.patch
@@ -6,8 +6,10 @@ Applied-Upstream: https://github.com/rvaser/spoa/pull/28
Last-Update: 2020-05-02
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- a/src/alignment_engine.cpp
-+++ b/src/alignment_engine.cpp
+Index: spoa.git/src/alignment_engine.cpp
+===================================================================
+--- spoa.git.orig/src/alignment_engine.cpp
++++ spoa.git/src/alignment_engine.cpp
@@ -3,6 +3,7 @@
#include "spoa/alignment_engine.hpp"
diff --git a/debian/patches/shared_and_static.patch b/debian/patches/shared_and_static.patch
index 1108ad5..cfbac69 100644
--- a/debian/patches/shared_and_static.patch
+++ b/debian/patches/shared_and_static.patch
@@ -2,8 +2,10 @@ Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 08 Jun 2018 13:20:51 +0200
Description: Build shared and static lib
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
+Index: spoa.git/CMakeLists.txt
+===================================================================
+--- spoa.git.orig/CMakeLists.txt
++++ spoa.git/CMakeLists.txt
@@ -21,7 +21,7 @@ endif ()
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
@@ -13,7 +15,7 @@ Description: Build shared and static lib
include(FetchContent)
include(GNUInstallDirs)
-@@ -181,7 +181,7 @@ if (spoa_build_tests)
+@@ -144,7 +144,7 @@ if (spoa_build_tests)
endif ()
endif ()
@@ -22,7 +24,7 @@ Description: Build shared and static lib
src/alignment_engine.cpp
src/graph.cpp
src/simd_alignment_engine_dispatcher.cpp
-@@ -200,9 +200,22 @@ if (spoa_use_cereal)
+@@ -163,9 +163,22 @@ if (spoa_use_cereal)
target_compile_definitions(spoa PUBLIC SPOA_USE_CEREAL)
endif ()
@@ -47,7 +49,7 @@ Description: Build shared and static lib
if (spoa_generate_dispatch)
list(APPEND ARCHITECTURES avx2 sse4.1 sse2)
-@@ -227,9 +240,15 @@ if (spoa_generate_dispatch)
+@@ -190,9 +203,15 @@ if (spoa_generate_dispatch)
spoa_avx2
spoa_sse4.1
spoa_sse2)
@@ -63,7 +65,7 @@ Description: Build shared and static lib
endif ()
if (spoa_install)
-@@ -246,6 +265,10 @@ if (spoa_install)
+@@ -209,6 +228,10 @@ if (spoa_install)
EXPORT ${PROJECT_NAME}Targets
DESTINATION ${CMAKE_INSTALL_LIBDIR})
install(
diff --git a/debian/patches/use_debian_packaged_libs.patch b/debian/patches/use_debian_packaged_libs.patch
index bc1f420..0b79e40 100644
--- a/debian/patches/use_debian_packaged_libs.patch
+++ b/debian/patches/use_debian_packaged_libs.patch
@@ -2,9 +2,11 @@ Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 08 Jun 2018 13:20:51 +0200
Description: Use Debian packaged libraries
Forwarded: not-needed
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -124,43 +124,6 @@
+Index: spoa.git/CMakeLists.txt
+===================================================================
+--- spoa.git.orig/CMakeLists.txt
++++ spoa.git/CMakeLists.txt
+@@ -124,43 +124,6 @@ if (spoa_use_cereal)
endif ()
endif ()
@@ -48,7 +50,7 @@ Forwarded: not-needed
if (spoa_build_tests)
find_package(GTest 1.10.0 QUIET)
if (NOT GTest_FOUND)
-@@ -264,8 +227,7 @@
+@@ -264,8 +227,7 @@ if (spoa_build_exe)
target_link_libraries(spoa_exe
spoa
@@ -58,7 +60,7 @@ Forwarded: not-needed
target_compile_definitions(spoa_exe PRIVATE VERSION="${PROJECT_VERSION}")
set_property(TARGET spoa_exe PROPERTY OUTPUT_NAME spoa)
-@@ -279,8 +241,7 @@
+@@ -279,8 +241,7 @@ if (spoa_build_tests)
target_link_libraries(spoa_test
spoa
Debdiff
[The following lists of changes regard files as different if they have different names, permissions or owners.]
Files in second set of .debs but not in first
-rw-r--r-- root/root /usr/lib/debug/.build-id/18/770accb9b6c768761db0af03e1040444b8ed81.debug
Files in first set of .debs but not in second
-rw-r--r-- root/root /usr/lib/debug/.build-id/81/f9e9a20cc744a272015e9a5fdd3a4dda0f7510.debug
No differences were encountered between the control files of package libspoa-dev
No differences were encountered between the control files of package libspoa7.0.0
No differences were encountered between the control files of package libspoa7.0.0-dbgsym
No differences were encountered between the control files of package spoa
Control files of package spoa-dbgsym: lines which differ (wdiff format)
Build-Ids: 81f9e9a20cc744a272015e9a5fdd3a4dda0f7510 18770accb9b6c768761db0af03e1040444b8ed81