[med-svn] [Git][med-team/libbioparser-dev][master] 4 commits: New upstream version 3.0.13
Michael R. Crusoe
gitlab at salsa.debian.org
Mon Mar 8 16:27:28 GMT 2021
Michael R. Crusoe pushed to branch master at Debian Med / libbioparser-dev
Commits:
e20f3084 by Michael R. Crusoe at 2021-03-08T17:10:31+01:00
New upstream version 3.0.13
- - - - -
97f583d4 by Michael R. Crusoe at 2021-03-08T17:10:31+01:00
routine-update: New upstream version
- - - - -
7c8cad5b by Michael R. Crusoe at 2021-03-08T17:10:33+01:00
Update upstream source from tag 'upstream/3.0.13'
Update to upstream version '3.0.13'
with Debian dir 70ead15372180e90f688efa36a756b1024c81969
- - - - -
0f8747db by Michael R. Crusoe at 2021-03-08T17:24:16+01:00
TODO: wait for libbiosoup-dev to enter the archive
- - - - -
11 changed files:
- .gitmodules
- .travis.yml
- CMakeLists.txt
- + Config.cmake.in
- README.md
- debian/changelog
- test/fasta_parser_test.cpp
- test/fastq_parser_test.cpp
- test/mhap_parser_test.cpp
- test/paf_parser_test.cpp
- test/sam_parser_test.cpp
Changes:
=====================================
.gitmodules
=====================================
@@ -1,4 +1,2 @@
-[submodule "vendor/biosoup"]
- path = vendor/biosoup
- url = https://github.com/rvaser/biosoup
+
=====================================
.travis.yml
=====================================
@@ -1,46 +1,39 @@
-dist: trusty
-
language: cpp
matrix:
include:
- - name: "GCC 4.8 (Linux)" # GCC 4.8.5 & CMake 3.9.2
+ - 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
- - cmake
env:
- SET_COMPILER="export CC=gcc-4.8 && export CXX=g++-4.8"
- - name: "Clang 3.5 (Linux)" # Clang 3.5.0 & CMake 3.9.2
+ - name: "Clang 3.5 (Linux)" # Clang 3.5.2 & CMake 3.12.4
os: linux
+ dist: xenial
addons:
apt:
- sources:
- - llvm-toolchain-trusty-3.5
packages:
- clang-3.5
- - cmake
env:
- SET_COMPILER="export CC=clang-3.5 && export CXX=clang++-3.5"
- - name: "Clang Xcode 9.0 (OSX)" # Clang 9.0.0 & CMake 3.9.2
+ - name: "Clang Xcode 9.4 (OSX)" # Clang 9.4.1 & CMake 3.15.5
os: osx
- osx_image: xcode9
+ osx_image: xcode9.4
before_install:
- eval "${SET_COMPILER}"
- - git clone https://github.com/google/googletest && cd googletest && mkdir build && cd build && git checkout 703bd9c
- - cmake -DCMAKE_CXX_FLAGS="-std=c++11" .. && make && sudo make install
- - cd ../../
install:
- mkdir build && cd build
- - cmake -Dbioparser_build_tests=ON -DCMAKE_BUILD_TYPE=Release .. && make
+ - cmake -DCMAKE_BUILD_TYPE=Release .. && make
script:
- ./bin/bioparser_test
=====================================
CMakeLists.txt
=====================================
@@ -1,6 +1,6 @@
-cmake_minimum_required(VERSION 3.9)
+cmake_minimum_required(VERSION 3.11)
-project(bioparser VERSION 3.0.12
+project(bioparser VERSION 3.0.13
LANGUAGES CXX
DESCRIPTION "Bioparser is a c++ header only parsing library for several formats in bioinformatics (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.")
@@ -13,31 +13,108 @@ set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin)
-find_package(ZLIB REQUIRED)
-add_library(${PROJECT_NAME} INTERFACE)
-target_link_libraries(${PROJECT_NAME} INTERFACE
- ZLIB::ZLIB)
+if (CMAKE_SOURCE_DIR STREQUAL PROJECT_SOURCE_DIR)
+ set(bioparser_main_project ON)
+endif ()
+option(bioparser_install "Generate install target" ${bioparser_main_project})
+option(bioparser_build_tests "Build unit tests" ${bioparser_main_project})
-target_include_directories(${PROJECT_NAME} INTERFACE
- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+find_package(ZLIB 1.2.8 REQUIRED)
-option(bioparser_build_tests "Build bioparser unit tests" OFF)
if (bioparser_build_tests)
- find_package(GTest REQUIRED)
- if (NOT TARGET biosoup)
- add_subdirectory(vendor/biosoup EXCLUDE_FROM_ALL)
+ find_package(biosoup 0.10.0 QUIET)
+ find_package(GTest 1.10.0 QUIET)
+
+ if (NOT biosoup_FOUND)
+ include(FetchContent)
+
+ FetchContent_Declare(
+ biosoup
+ GIT_REPOSITORY https://github.com/rvaser/biosoup
+ GIT_TAG 0.10.0)
+
+ FetchContent_GetProperties(biosoup)
+ if (NOT biosoup_POPULATED)
+ FetchContent_Populate(biosoup)
+ add_subdirectory(
+ ${biosoup_SOURCE_DIR}
+ ${biosoup_BINARY_DIR}
+ EXCLUDE_FROM_ALL)
+ endif ()
endif ()
- add_executable(${PROJECT_NAME}_test
+
+ if (NOT GTest_FOUND)
+ include(FetchContent)
+
+ FetchContent_Declare(
+ googletest
+ GIT_REPOSITORY https://github.com/google/googletest
+ GIT_TAG release-1.10.0)
+
+ FetchContent_GetProperties(googletest)
+ if (NOT googletest_POPULATED)
+ FetchContent_Populate(googletest)
+ add_subdirectory(
+ ${googletest_SOURCE_DIR}
+ ${googletest_BINARY_DIR}
+ EXCLUDE_FROM_ALL)
+ add_library(GTest::Main ALIAS gtest_main)
+ endif ()
+ endif ()
+endif ()
+
+add_library(bioparser INTERFACE)
+add_library(${PROJECT_NAME}::bioparser ALIAS bioparser)
+
+target_include_directories(bioparser INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+ $<INSTALL_INTERFACE:include>)
+
+target_link_libraries(bioparser INTERFACE
+ ZLIB::ZLIB)
+
+if (bioparser_install)
+ include(GNUInstallDirs)
+ include(CMakePackageConfigHelpers)
+
+ configure_package_config_file(
+ ${CMAKE_CURRENT_SOURCE_DIR}/Config.cmake.in
+ ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake
+ INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
+ write_basic_package_version_file(
+ ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake
+ COMPATIBILITY SameMajorVersion)
+
+ install(
+ TARGETS bioparser
+ EXPORT ${PROJECT_NAME}Targets)
+ install(
+ DIRECTORY include/bioparser
+ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+ install(
+ EXPORT ${PROJECT_NAME}Targets
+ NAMESPACE ${PROJECT_NAME}::
+ DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
+ install(
+ FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake
+ ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake
+ DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
+endif ()
+
+if (bioparser_build_tests)
+ add_executable(bioparser_test
test/parser_test.cpp
test/fasta_parser_test.cpp
test/fastq_parser_test.cpp
test/mhap_parser_test.cpp
test/paf_parser_test.cpp
test/sam_parser_test.cpp)
- target_link_libraries(${PROJECT_NAME}_test
- ${PROJECT_NAME}
- biosoup
+
+ target_link_libraries(bioparser_test
+ bioparser
+ biosoup::biosoup
GTest::Main)
- target_compile_definitions(${PROJECT_NAME}_test PRIVATE
- BIOPARSER_DATA_PATH="${PROJECT_SOURCE_DIR}/test/data/")
+
+ target_compile_definitions(bioparser_test
+ PRIVATE TEST_DATA="${PROJECT_SOURCE_DIR}/test/data/")
endif ()
=====================================
Config.cmake.in
=====================================
@@ -0,0 +1,7 @@
+ at PACKAGE_INIT@
+
+include(CMakeFindDependencyMacro)
+find_dependency(ZLIB)
+
+include("${CMAKE_CURRENT_LIST_DIR}/@PROJECT_NAME at Targets.cmake")
+check_required_components("@PROJECT_NAME@")
=====================================
README.md
=====================================
@@ -3,28 +3,47 @@
[](https://github.com/rvaser/bioparser/releases/latest)
[](https://travis-ci.com/rvaser/bioparser)
-Bioparser is a c++ header only parsing library for several formats in bioinformatics (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.
+Bioparser is a c++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files..
## Usage
-If you would like to add bioparser to your project via CMake, add the following:
+To build bioparser run the following commands:
+```bash
+git clone https://github.com/rvaser/bioparser && cd bioparser && mkdir build && cd build
+cmake -DCMAKE_BUILD_TYPE=Release .. && make
+```
+which will create install targets and unit tests. Running `make install` will create a package on your system that can be searched and linked with:
+```cmake
+find_package(bioparser)
+target_link_libraries(<target> bioparser::bioparser)
+```
+On the other hand, you can include bioparser as a submodule and add it to your project with the following:
```cmake
if (NOT TARGET bioparser)
add_subdirectory(<path_to_submodules>/bioparser EXCLUDE_FROM_ALL)
endif ()
-target_link_libraries(<your_exe> bioparser)
+target_link_libraries(<target> bioparser::bioparser)
```
If you are not using CMake, include the appropriate header file directly to your project and link with zlib.
+#### Build options
+
+- `bioparser_install`: generate install target
+- `bioparser_build_tests`: build unit tests
+
#### Dependencies
-- gcc 4.8+ or clang 3.5+
-- (optional) cmake 3.9+
-- zlib
+- gcc 4.8+ | clang 3.5+
+- zlib 1.2.8+
+- (optional) cmake 3.11+
+
+###### Hidden
+- (bioparser_test) biosoup 0.10.0
+- (bioparser_test) googletest 1.10.0
## Examples
-### FASTA parser
+#### FASTA parser
```cpp
#include "bioparser/fasta_parser.hpp"
@@ -43,7 +62,7 @@ auto p = bioparser::Parser<Sequence>::Create<bioparser::FastaParser>(path);
auto s = p->Parse(-1);
```
-### FASTQ parser
+#### FASTQ parser
```cpp
#include "bioparser/fastq_parser.hpp"
@@ -61,16 +80,19 @@ auto p = bioparser::Parser<Sequence>::Create<bioparser::FastqParser>(path);
// parse in chunks
std::vector<std::unique_ptr<Sequence>> s;
-std::uint32_t chunk_size = 500 * 1024 * 1024; // 500 MB
-for (auto t = p->parse(chunk_size); !t.empty(); t = p->parse(chunk_size)) {
+while (true) {
+ auto c = p->Parse(1ULL << 30); // 1 GB
+ if (c.empty()) {
+ break;
+ }
s.insert(
s.end(),
- std::make_move_iterator(t.begin()),
- std::make_move_iterator(t.end()));
+ std::make_move_iterator(c.begin()),
+ std::make_move_iterator(c.end()));
}
```
-### MHAP parser
+#### MHAP parser
```cpp
#include "bioparser/mhap_parser.hpp"
@@ -99,7 +121,7 @@ auto p = bioparser::Parser<Overlap>::Create<bioparser::MhapParser>(path);
auto o = p->Parse(-1);
```
-### PAF parser
+#### PAF parser
```cpp
#include "bioparser/paf_parser.hpp"
@@ -128,7 +150,7 @@ auto p = bioparser::Parser<Overlap>::Create<bioparser::PafParser>(path);
auto o = p->Parse(-1);
```
-### SAM parser
+#### SAM parser
```cpp
#include "bioparser/sam_parser.hpp"
@@ -166,20 +188,6 @@ friend bioparser::PafParser<Overlap>;
friend bioparser::SamParser<Overlap>;
```
-## Unit tests
-
-To build and run bioparser unit tests run the following commands:
-
-```bash
-git clone --recursive https://github.com/rvaser/bioparser.git bioparser
-cd bioparser && mkdir build && cd build
-cmake -Dbioparser_build_tests=ON -DCMAKE_BUILD_TYPE=Release .. && make
-./bin/bioparser_test
-```
-
-#### Dependencies
-- gtest
-
## Acknowledgement
This work has been supported in part by the Croatian Science Foundation under the project Single genome and metagenome assembly (IP-2018-01-5886)..
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+libbioparser-dev (3.0.13-1) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ TODO: wait for libbiosoup-dev to enter the archive
+
+ -- Michael R. Crusoe <crusoe at debian.org> Mon, 08 Mar 2021 17:10:31 +0100
+
libbioparser-dev (3.0.12-1) unstable; urgency=medium
[ Étienne Mollier ]
=====================================
test/fasta_parser_test.cpp
=====================================
@@ -15,7 +15,7 @@ namespace test {
class BioparserFastaTest: public ::testing::Test {
public:
void Setup(const std::string& file) {
- p = Parser<biosoup::Sequence>::Create<FastaParser>(BIOPARSER_DATA_PATH + file); // NOLINT
+ p = Parser<biosoup::Sequence>::Create<FastaParser>(TEST_DATA + file);
}
void Check(bool is_trimmed = true) {
=====================================
test/fastq_parser_test.cpp
=====================================
@@ -13,7 +13,7 @@ namespace test {
class BioparserFastqTest: public ::testing::Test {
public:
void Setup(const std::string& file) {
- p = Parser<biosoup::Sequence>::Create<FastqParser>(BIOPARSER_DATA_PATH + file); // NOLINT
+ p = Parser<biosoup::Sequence>::Create<FastqParser>(TEST_DATA + file);
}
void Check() {
=====================================
test/mhap_parser_test.cpp
=====================================
@@ -43,7 +43,7 @@ struct MhapOverlap: public biosoup::Overlap {
class BioparserMhapTest: public ::testing::Test {
public:
void Setup(const std::string& file) {
- p = Parser<MhapOverlap>::Create<MhapParser>(BIOPARSER_DATA_PATH + file);
+ p = Parser<MhapOverlap>::Create<MhapParser>(TEST_DATA + file);
}
void Check() {
=====================================
test/paf_parser_test.cpp
=====================================
@@ -49,7 +49,7 @@ struct PafOverlap: public biosoup::Overlap {
class BioparserPafTest: public ::testing::Test {
public:
void Setup(const std::string& file) {
- p = Parser<PafOverlap>::Create<PafParser>(BIOPARSER_DATA_PATH + file);
+ p = Parser<PafOverlap>::Create<PafParser>(TEST_DATA + file);
}
void Check() {
=====================================
test/sam_parser_test.cpp
=====================================
@@ -54,7 +54,7 @@ struct SamOverlap: public biosoup::Overlap {
class BioparserSamTest: public ::testing::Test {
public:
void Setup(const std::string& file) {
- p = Parser<SamOverlap>::Create<SamParser>(BIOPARSER_DATA_PATH + file);
+ p = Parser<SamOverlap>::Create<SamParser>(TEST_DATA + file);
}
void Check() {
View it on GitLab: https://salsa.debian.org/med-team/libbioparser-dev/-/compare/25019bc7f8e0a494cac063d6e9e65628463e1e64...0f8747db179d1b7abcbce1957928320c52182ef7
--
View it on GitLab: https://salsa.debian.org/med-team/libbioparser-dev/-/compare/25019bc7f8e0a494cac063d6e9e65628463e1e64...0f8747db179d1b7abcbce1957928320c52182ef7
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