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Tbrekalo/1.8.2 #63

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e5db801
added cmake deps for cxxopts and tsl-robin-map
tbrekalo May 23, 2022
469596a
refactored command line parsing; added project version config
tbrekalo May 23, 2022
8f9bb50
refactored sequence loading; not has multithreades support and recusi…
tbrekalo May 23, 2022
a946839
style change
tbrekalo May 23, 2022
42879d4
swaped std::unordered_set with tsl::robin_set; removed unnecessary ce…
tbrekalo May 23, 2022
ca27b63
bumped version in cmake to 1.8.2
tbrekalo May 23, 2022
6f177dc
updated overlap selectoin
tbrekalo Jun 13, 2022
8c62ee9
overlap selection updated
tbrekalo Jun 13, 2022
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2 changes: 1 addition & 1 deletion CMakeLists.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
cmake_minimum_required(VERSION 3.11)
project(raven
VERSION 1.8.1
VERSION 1.8.2
LANGUAGES CXX
DESCRIPTION "Raven is a de novo genome assembler for long uncorrected reads.")

Expand Down
48 changes: 48 additions & 0 deletions Raven.deps.cmake
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Original file line number Diff line number Diff line change
@@ -1,6 +1,20 @@
include(FetchContent)
include(GNUInstallDirs)

FetchContent_Declare(
ram
GIT_REPOSITORY https://github.com/tbrekalo/ram-experimental
GIT_TAG f7042c21fee01feb87e1953e498c402eb1f8fcc6)

FetchContent_GetProperties(ram)
if (NOT ram_POPULATED)
FetchContent_Populate(ram)
add_subdirectory(
${ram_SOURCE_DIR}
${ram_BINARY_DIR}
EXCLUDE_FROM_ALL)
endif ()

find_package(bioparser 3.0.13 QUIET)
if (NOT bioparser_FOUND)
FetchContent_Declare(
Expand Down Expand Up @@ -53,6 +67,40 @@ if (NOT racon_FOUND)
endif ()
endif ()

find_package(cxxopts 3.0.0 QUIET)
if (NOT cxxopts_FOUND)
FetchContent_Declare(
cxxopts
GIT_REPOSITORY https://github.com/jarro2783/cxxopts.git
GIT_TAG v3.0.0)

FetchContent_GetProperties(cxxopts)
if (NOT cxxopts_POPULATED)
FetchContent_Populate(cxxopts)
add_subdirectory(
${cxxopts_SOURCE_DIR}
${cxxopts_BINARY_DIR}
EXCLUDE_FROM_ALL)
endif ()
endif ()

find_package(tsl-robin-map 1.0.1 QUIET)
if (NOT tsl-robin-map_FOUND)
FetchContent_Declare(
tsl-robin-map
GIT_REPOSITORY https://github.com/Tessil/robin-map.git
GIT_TAG v1.0.1)

FetchContent_GetProperties(tsl-robin-map)
if (NOT tsl-robin-map_POPULATED)
FetchContent_Populate(tsl-robin-map)
add_subdirectory(
${tsl-robin-map_SOURCE_DIR}
${tsl-robin-map_BINARY_DIR}
EXCLUDE_FROM_ALL)
endif ()
endif ()

if (RAVEN_BUILD_PYTHON)
find_package(pybind11 QUIET)
if (NOT pybind11_FOUND)
Expand Down
5 changes: 4 additions & 1 deletion RavenExe/Exe.cmake
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ if (NOT TARGET RavenExe)
include(${CMAKE_CURRENT_LIST_DIR}/Exe.srcs.cmake)

add_executable(raven_exe ${SOURCES})
target_link_libraries(raven_exe PRIVATE raven)
target_link_libraries(raven_exe PRIVATE cxxopts::cxxopts raven)

if (racon_enable_cuda)
target_compile_definitions(raven_exe PRIVATE CUDA_ENABLED)
Expand All @@ -12,4 +12,7 @@ if (NOT TARGET RavenExe)
target_compile_definitions(raven_exe PRIVATE VERSION="${PROJECT_VERSION}")
set_property(TARGET raven_exe PROPERTY OUTPUT_NAME raven)

configure_file(
"${CMAKE_CURRENT_LIST_DIR}/src/raven_cfg.h.in" raven_cfg.h)
target_include_directories(raven_exe PRIVATE ${PROJECT_BINARY_DIR})
endif()
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