[med-svn] [Git][med-team/racon][master] 5 commits: New upstream version 1.5.0
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sun Dec 19 18:17:01 GMT 2021
Nilesh Patra pushed to branch master at Debian Med / racon
Commits:
7f70823e by Nilesh Patra at 2021-12-19T18:16:43+00:00
New upstream version 1.5.0
- - - - -
bf039fc2 by Nilesh Patra at 2021-12-19T18:16:43+00:00
Refresh d/p/{py3,remove_buildpath}
- - - - -
d5f1f039 by Nilesh Patra at 2021-12-19T18:16:43+00:00
Re-write use_debian_packaged_libs.patch to use libs present in Debian
- - - - -
928a54fb by Nilesh Patra at 2021-12-19T18:16:43+00:00
Add patch to make package compatible with older libthreadpool
- - - - -
ff3662b4 by Nilesh Patra at 2021-12-19T18:16:43+00:00
[ci skip] Interim changelog
- - - - -
20 changed files:
- + .github/workflows/racon.yml
- − .travis.yml
- CMakeLists.txt
- Makefile
- README.md
- debian/changelog
- + debian/patches/make-compatible-with-old-threadpool.patch
- debian/patches/py3
- debian/patches/remove_buildpath
- debian/patches/series
- debian/patches/use_debian_packaged_libs.patch
- meson.build
- scripts/racon_wrapper.py
- src/cuda/cudapolisher.cpp
- src/main.cpp
- src/polisher.cpp
- test/meson.build
- test/racon_test.cpp
- − test/racon_test_config.h.in
- vendor/meson.build
Changes:
=====================================
.github/workflows/racon.yml
=====================================
@@ -0,0 +1,53 @@
+name: racon CI
+
+on:
+ push:
+ pull_request:
+ branches:
+ - master
+
+env:
+ BUILD_TYPE: Release
+
+jobs:
+ test:
+ strategy:
+ matrix:
+ compiler:
+ - g++
+ - g++-4.8
+ - clang++
+ - clang++-4.0
+
+ runs-on: ubuntu-18.04
+
+ steps:
+ - uses: actions/checkout at v2
+
+ - if: ${{ matrix.compiler == 'g++-4.8' }}
+ name: Setup GCC
+ uses: egor-tensin/setup-gcc at v1
+ with:
+ version: "4.8"
+ platform: x64
+
+ - if: ${{ matrix.compiler == 'clang++-4.0' }}
+ name: Setup Clang
+ uses: egor-tensin/setup-clang at v1
+ with:
+ version: "4.0"
+ platform: x64
+
+ - name: Configure CMake
+ run: cmake -B ${{ github.workspace }}/build -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }}
+ env:
+ CXX: ${{ matrix.compiler }}
+
+ - name: Build
+ run: cmake --build ${{ github.workspace }}/build --config ${{ env.BUILD_TYPE }}
+
+ - name: Test
+ working-directory: ${{ github.workspace }}/build
+ run: |
+ bin/racon --version
+ bin/racon_test
=====================================
.travis.yml deleted
=====================================
@@ -1,47 +0,0 @@
-dist: trusty
-
-language: cpp
-
-matrix:
- include:
- - name: "GCC 4.8 (Linux)" # GCC 4.8.5 & CMake 3.9.2
- os: linux
- addons:
- apt:
- sources:
- - ubuntu-toolchain-r-test
- packages:
- - g++-4.8
- - cmake
- env:
- - SET_COMPILER="export CC=gcc-4.8 && export CXX=g++-4.8"
-
- - name: "Clang 3.5 (Linux)" # Clang 3.5.0 & CMake 3.9.2
- os: linux
- addons:
- apt:
- sources:
- - llvm-toolchain-trusty-3.5
- packages:
- - clang-3.5
- - cmake
- env:
- - SET_COMPILER="export CC=clang-3.5 && export CXX=clang++-3.5"
-
-before_install:
- - eval "${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 -Dspoa_build_executable=ON -Dracon_build_tests=ON -Dracon_build_wrapper=ON -DCMAKE_BUILD_TYPE=Release .. && make
-
-script:
- - ./bin/racon --version
- - ./bin/racon_test
-
-notifications:
- email:
- on_failure: always
=====================================
CMakeLists.txt
=====================================
@@ -1,147 +1,266 @@
-cmake_minimum_required(VERSION 3.2)
-project(racon)
-set(racon_version 1.4.21)
+cmake_minimum_required(VERSION 3.11)
-set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
-set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
-set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin)
+project(racon VERSION 1.5.0
+ LANGUAGES CXX
+ DESCRIPTION "Racon is a consensus module for de novo genome assembly.")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -pedantic")
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
-option(racon_build_tests "Build racon unit tests" OFF)
-option(racon_build_wrapper "Build racon wrapper" OFF)
-option(racon_enable_cuda "Build racon with NVIDIA CUDA support" OFF)
-
-# Check CUDA compatibility.
-if(racon_enable_cuda)
- find_package(CUDA 9.0 QUIET REQUIRED)
- if(NOT ${CUDA_FOUND})
- message(FATAL_ERROR "CUDA not detected on system. Please install")
- else()
- message(STATUS "Using CUDA ${CUDA_VERSION} from ${CUDA_TOOLKIT_ROOT_DIR}")
- set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS} -lineinfo")
- endif()
-endif()
+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)
+
+include(FetchContent)
+include(GNUInstallDirs)
+
+if (CMAKE_SOURCE_DIR STREQUAL PROJECT_SOURCE_DIR)
+ set(racon_main_project ON)
+endif ()
+option(racon_build_tests "Build unit tests" ${racon_main_project})
+option(racon_build_wrapper "Build wrapper" OFF)
+option(racon_enable_cuda "Build with NVIDIA CUDA support" OFF)
+
+find_package(bioparser 3.0.15 QUIET)
+if (NOT bioparser_FOUND)
+ FetchContent_Declare(
+ bioparser
+ GIT_REPOSITORY https://github.com/rvaser/bioparser
+ GIT_TAG 3.0.15)
+
+ FetchContent_GetProperties(bioparser)
+ if (NOT bioparser_POPULATED)
+ FetchContent_Populate(bioparser)
+ add_subdirectory(
+ ${bioparser_SOURCE_DIR}
+ ${bioparser_BINARY_DIR}
+ EXCLUDE_FROM_ALL)
+ endif ()
+endif ()
+
+find_package(edlib 1.2.7 QUIET)
+if (NOT edlib_FOUND)
+ FetchContent_Declare(
+ edlib
+ GIT_REPOSITORY https://github.com/martinsos/edlib
+ GIT_TAG v1.2.7)
+
+ FetchContent_GetProperties(edlib)
+ if (NOT edlib_POPULATED)
+ FetchContent_Populate(edlib)
+ add_subdirectory(
+ ${edlib_SOURCE_DIR}
+ ${edlib_BINARY_DIR}
+ EXCLUDE_FROM_ALL)
+ endif ()
+endif ()
+
+find_package(spoa 4.0.8 QUIET)
+if (NOT spoa_FOUND)
+ FetchContent_Declare(
+ spoa
+ GIT_REPOSITORY https://github.com/rvaser/spoa
+ GIT_TAG 4.0.8)
+
+ FetchContent_GetProperties(spoa)
+ if (NOT spoa_POPULATED)
+ FetchContent_Populate(spoa)
+ add_subdirectory(
+ ${spoa_SOURCE_DIR}
+ ${spoa_BINARY_DIR}
+ EXCLUDE_FROM_ALL)
+ endif ()
+endif ()
+
+find_package(thread_pool 4.0.0 QUIET)
+if (NOT thread_pool_FOUND)
+ FetchContent_Declare(
+ thread_pool
+ GIT_REPOSITORY https://github.com/rvaser/thread_pool
+ GIT_TAG 4.0.0)
+
+ FetchContent_GetProperties(thread_pool)
+ if (NOT thread_pool_POPULATED)
+ FetchContent_Populate(thread_pool)
+ add_subdirectory(
+ ${thread_pool_SOURCE_DIR}
+ ${thread_pool_BINARY_DIR}
+ EXCLUDE_FROM_ALL)
+ endif ()
+endif ()
+
+if (racon_build_tests)
+ find_package(GTest 1.10.0 QUIET)
+ if (NOT GTest_FOUND)
+ 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}
+ ${googletest_BINARY_DIR}
+ EXCLUDE_FROM_ALL)
+ add_library(GTest::Main ALIAS gtest_main)
+ endif ()
+ endif ()
+endif ()
+
+if (racon_build_wrapper)
+ find_package(rampler 2.0.0 QUIET)
+ if (NOT rampler_FOUND)
+ FetchContent_Declare(
+ rampler
+ GIT_REPOSITORY https://github.com/rvaser/rampler
+ GIT_TAG 2.0.0)
-include_directories(${PROJECT_SOURCE_DIR}/src)
+ FetchContent_GetProperties(rampler)
+ if (NOT rampler_POPULATED)
+ FetchContent_Populate(rampler)
+ add_subdirectory(
+ ${rampler_SOURCE_DIR}
+ ${rampler_BINARY_DIR})
+ endif ()
+ endif ()
+endif ()
+
+if (racon_enable_cuda)
+ find_package(CUDA 9.0 QUIET REQUIRED)
+ if (NOT ${CUDA_FOUND})
+ message(FATAL_ERROR "CUDA not detected on system. Please install")
+ else ()
+ message(STATUS "Using CUDA ${CUDA_VERSION} from ${CUDA_TOOLKIT_ROOT_DIR}")
+ set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS} -lineinfo")
+ endif ()
+ if (DEFINED CLARAGENOMICSANALYSIS_SDK_PATH)
+ list(APPEND CMAKE_PREFIX_PATH "${CLARAGENOMICSANALYSIS_SDK_PATH}/cmake")
+ find_package(cudapoa REQUIRED)
+ find_package(cudaaligner REQUIRED)
+ elseif (DEFINED CLARAGENOMICSANALYSIS_SRC_PATH)
+ if (NOT TARGET cudapoa)
+ add_subdirectory(
+ ${CLARAGENOMICSANALYSIS_SRC_PATH}
+ ${CMAKE_CURRENT_BINARY_DIR}/GenomeWorks
+ EXCLUDE_FROM_ALL)
+ endif ()
+ if (NOT TARGET cudaaligner)
+ add_subdirectory(
+ ${CLARAGENOMICSANALYSIS_SRC_PATH}
+ ${CMAKE_CURRENT_BINARY_DIR}/GenomeWorks
+ EXCLUDE_FROM_ALL)
+ endif ()
+ else ()
+ FetchContent_Declare(
+ genomeworks
+ GIT_REPOSITORY https://github.com/clara-parabricks/GenomeWorks
+ GIT_TAG v0.5.3)
+
+ FetchContent_GetProperties(genomeworks)
+ if (NOT genomeworks_POPULATED)
+ FetchContent_Populate(genomeworks)
+ add_subdirectory(
+ ${genomeworks_SOURCE_DIR}
+ ${genomeworks_BINARY_DIR}
+ EXCLUDE_FROM_ALL)
+ endif ()
+ endif ()
+endif ()
set(racon_sources
- src/main.cpp
- src/logger.cpp
- src/polisher.cpp
- src/overlap.cpp
- src/sequence.cpp
- src/window.cpp)
-
-if(racon_enable_cuda)
- list(APPEND racon_sources src/cuda/cudapolisher.cpp src/cuda/cudabatch.cpp src/cuda/cudaaligner.cpp)
- cuda_add_executable(racon ${racon_sources})
- target_compile_definitions(racon PRIVATE CUDA_ENABLED)
-else()
- add_executable(racon ${racon_sources})
-endif()
+ src/logger.cpp
+ src/polisher.cpp
+ src/overlap.cpp
+ src/sequence.cpp
+ src/window.cpp)
-# Add version information to bibary.
-target_compile_definitions(racon PRIVATE RACON_VERSION="v${racon_version}")
+if (racon_enable_cuda)
+ include_directories(${PROJECT_SOURCE_DIR}/src)
+ list(APPEND racon_sources
+ src/cuda/cudapolisher.cpp
+ src/cuda/cudabatch.cpp
+ src/cuda/cudaaligner.cpp)
+
+ cuda_add_library(racon
+ ${racon_sources})
+
+ target_compile_definitions(racon
+ PRIVATE CUDA_ENABLED)
+else ()
+ add_library(racon
+ ${racon_sources})
+endif ()
+
+target_link_libraries(racon
+ bioparser::bioparser
+ edlib::edlib
+ spoa::spoa
+ thread_pool::thread_pool)
-if (NOT TARGET bioparser)
- add_subdirectory(vendor/spoa/vendor/bioparser EXCLUDE_FROM_ALL)
-endif()
-if (NOT TARGET spoa)
- add_subdirectory(vendor/spoa EXCLUDE_FROM_ALL)
-endif()
-if (NOT TARGET thread_pool)
- add_subdirectory(vendor/thread_pool EXCLUDE_FROM_ALL)
-endif()
-if (NOT TARGET edlib)
- add_subdirectory(vendor/edlib EXCLUDE_FROM_ALL)
-endif()
if (racon_enable_cuda)
- if (DEFINED CLARAGENOMICSANALYSIS_SDK_PATH)
- list(APPEND CMAKE_PREFIX_PATH "${CLARAGENOMICSANALYSIS_SDK_PATH}/cmake")
- find_package(cudapoa REQUIRED)
- find_package(cudaaligner REQUIRED)
- elseif (DEFINED CLARAGENOMICSANALYSIS_SRC_PATH)
- if (NOT TARGET cudapoa)
- add_subdirectory(${CLARAGENOMICSANALYSIS_SRC_PATH} ${CMAKE_CURRENT_BINARY_DIR}/GenomeWorks EXCLUDE_FROM_ALL)
- endif()
- if (NOT TARGET cudaaligner)
- add_subdirectory(${CLARAGENOMICSANALYSIS_SRC_PATH} ${CMAKE_CURRENT_BINARY_DIR}/GenomeWorks EXCLUDE_FROM_ALL)
- endif()
- elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/vendor/GenomeWorks)
- if (NOT TARGET cudapoa)
- add_subdirectory(vendor/GenomeWorks ${CMAKE_CURRENT_BINARY_DIR}/GenomeWorks EXCLUDE_FROM_ALL)
- endif()
- if (NOT TARGET cudaaligner)
- add_subdirectory(vendor/GenomeWorks ${CMAKE_CURRENT_BINARY_DIR}/GenomeWorks EXCLUDE_FROM_ALL)
- endif()
- else()
- if (NOT TARGET cudapoa)
- add_subdirectory(../GenomeWorks ${CMAKE_CURRENT_BINARY_DIR}/GenomeWorks EXCLUDE_FROM_ALL)
- endif()
- if (NOT TARGET cudaaligner)
- add_subdirectory(../GenomeWorks ${CMAKE_CURRENT_BINARY_DIR}/GenomeWorks EXCLUDE_FROM_ALL)
- endif()
- endif()
-endif()
+ target_link_libraries(racon
+ cudapoa
+ cudaaligner)
+endif ()
+
+target_include_directories(racon PUBLIC
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/src>)
+
+add_executable(racon_exe
+ src/main.cpp)
+
+target_link_libraries(racon_exe
+ racon)
-target_link_libraries(racon bioparser spoa thread_pool edlib_static)
if (racon_enable_cuda)
- target_link_libraries(racon cudapoa cudaaligner)
-endif()
+ target_compile_definitions(racon_exe
+ PRIVATE CUDA_ENABLED)
+endif ()
+
+target_compile_definitions(racon_exe PRIVATE VERSION="${PROJECT_VERSION}")
+set_property(TARGET racon_exe PROPERTY OUTPUT_NAME racon)
-install(TARGETS racon DESTINATION bin)
+install(TARGETS racon_exe DESTINATION ${CMAKE_INSTALL_BINDIR})
if (racon_build_tests)
- find_package(GTest REQUIRED)
- set(racon_test_data_path ${PROJECT_SOURCE_DIR}/test/data/)
- configure_file("${PROJECT_SOURCE_DIR}/test/racon_test_config.h.in"
- "${PROJECT_BINARY_DIR}/config/racon_test_config.h")
- include_directories(${PROJECT_BINARY_DIR}/config)
- include_directories(${PROJECT_SOURCE_DIR}/src)
-
- set(racon_test_sources
- test/racon_test.cpp
- src/logger.cpp
- src/polisher.cpp
- src/overlap.cpp
- src/sequence.cpp
- src/window.cpp)
-
- if (racon_enable_cuda)
- list(APPEND racon_test_sources src/cuda/cudapolisher.cpp src/cuda/cudabatch.cpp src/cuda/cudaaligner.cpp)
- cuda_add_executable(racon_test ${racon_test_sources})
- target_compile_definitions(racon_test PRIVATE CUDA_ENABLED)
- else()
- add_executable(racon_test ${racon_test_sources})
- endif()
-
- target_link_libraries(racon_test bioparser spoa thread_pool edlib_static GTest::Main)
- if (racon_enable_cuda)
- target_link_libraries(racon_test cudapoa cudaaligner)
- endif()
+ add_executable(racon_test
+ test/racon_test.cpp)
+
+ target_link_libraries(racon_test
+ racon
+ GTest::Main)
+
+ target_compile_definitions(racon_test
+ PRIVATE TEST_DATA="${PROJECT_SOURCE_DIR}/test/data/")
+
+ if (racon_enable_cuda)
+ target_compile_definitions(racon_test
+ PRIVATE CUDA_ENABLED)
+ endif ()
endif()
if (racon_build_wrapper)
- set(racon_path ${PROJECT_BINARY_DIR}/bin/racon)
- set(rampler_path ${PROJECT_BINARY_DIR}/vendor/rampler/bin/rampler)
- configure_file(${PROJECT_SOURCE_DIR}/scripts/racon_wrapper.py
- ${PROJECT_BINARY_DIR}/${CMAKE_FILES_DIRECTORY}/racon_wrapper)
- file(COPY ${PROJECT_BINARY_DIR}/${CMAKE_FILES_DIRECTORY}/racon_wrapper
- DESTINATION ${PROJECT_BINARY_DIR}/bin
- FILE_PERMISSIONS OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE
- WORLD_READ WORLD_EXECUTE)
-
- if (NOT TARGET rampler)
- add_subdirectory(vendor/rampler)
- endif()
+ set(racon_path ${PROJECT_BINARY_DIR}/bin/racon)
+ set(rampler_path ${PROJECT_BINARY_DIR}/_deps/rampler-build/bin/rampler)
+ if (racon_enable_cuda)
+ set(racon_wrapper_enable_cuda True)
+ else ()
+ set(racon_wrapper_enable_cuda False)
+ endif ()
+ configure_file(${PROJECT_SOURCE_DIR}/scripts/racon_wrapper.py
+ ${PROJECT_BINARY_DIR}/${CMAKE_FILES_DIRECTORY}/racon_wrapper)
+ file(COPY ${PROJECT_BINARY_DIR}/${CMAKE_FILES_DIRECTORY}/racon_wrapper
+ DESTINATION ${PROJECT_BINARY_DIR}/bin
+ FILE_PERMISSIONS OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE
+ WORLD_READ WORLD_EXECUTE)
endif()
# Add Debian packaging
SET(CPACK_GENERATOR "DEB")
SET(CPACK_DEBIAN_PACKAGE_MAINTAINER "Robert Vaser")
-set(CPACK_PACKAGE_VERSION "${racon_version}")
+set(CPACK_PACKAGE_VERSION "${PROJECT_VERSION}")
include(CPack)
=====================================
Makefile
=====================================
@@ -1,29 +1,31 @@
-.PHONY: all clean meson cmake debug dist modules
+.PHONY: all clean meson cmake debug dist
all: meson
clean:
rm -rf build build-meson
-meson: modules
+VENDOR_FILES=vendor/thread_pool/README.md vendor/spoa/README.md vendor/rampler/README.md vendor/GenomeWorks/README.md
+
+meson: ${VENDOR_FILES}
@echo "[Invoking Meson]"
@mkdir -p build-meson && cd build-meson && meson --buildtype=release -Dc_args=-O3 -Dtests=true && ninja
-rebuild: modules
+rebuild: ${VENDOR_FILES}
@echo "[Running Ninja only]"
@ninja -C build-meson
-cmake: modules
+cmake: ${VENDOR_FILES}
@echo "[Invoking CMake]"
@mkdir -p build && cd build && cmake -DCMAKE_BUILD_TYPE=Release -Dracon_build_tests=ON .. && make
-debug: modules
+debug: ${VENDOR_FILES}
@echo "[Invoking Meson]"
@mkdir -p build-debug && cd build-debug && (meson --buildtype=debugoptimized -Db_sanitize=address -Dtests=true) && ninja
dist: release
cd build && ninja-dist
-modules:
+vendor/%/README.md:
@echo "[Fetching submodules]"
@git submodule update --init
=====================================
README.md
=====================================
@@ -9,7 +9,7 @@ Consensus module for raw de novo DNA assembly of long uncorrected reads.
## Description
Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.
-Racon can be used as a polishing tool after the assembly with **either Illumina data or data produced by third generation of sequencing**. The type of data inputed is automatically detected.
+Racon can be used as a polishing tool after the assembly with either **short accurate data** or **data produced by third generation of sequencing**. The type of data inputted is automatically detected. Although, Racon expects single-end short reads, while paired-end reads should be renamed with unique names up to the first whitespace and joined into a single file before mapping (which can be done with misc/racon_preprocess.py).
Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. All input files **can be compressed with gzip** (which will have impact on parsing time).
@@ -31,22 +31,14 @@ A **wrapper script** is also available to enable easier usage to the end-user fo
To install Racon run the following commands:
```bash
-git clone --recursive https://github.com/lbcb-sci/racon.git racon
-cd racon
-mkdir build
-cd build
-cmake -DCMAKE_BUILD_TYPE=Release ..
-make
+git clone https://github.com/lbcb-sci/racon && cd racon && mkdir build && cd build
+cmake -DCMAKE_BUILD_TYPE=Release .. && make
```
-After successful installation, an executable named `racon` will appear in `build/bin`.
+After successful installation, an executable named `racon` will appear in `build/bin` (alongside unit tests `racon_test`).
Optionally, you can run `sudo make install` to install racon executable to your machine.
-***Note***: if you omitted `--recursive` from `git clone`, run `git submodule update --init --recursive` before proceeding with compilation.
-
-To build unit tests add `-Dracon_build_tests=ON` while running `cmake` (Gtest required). After installation, an executable named `racon_test` will be created in `build/bin`.
-
To build the wrapper script add `-Dracon_build_wrapper=ON` while running `cmake`. After installation, an executable named `racon_wrapper` (python script) will be created in `build/bin`.
### CUDA Support
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+racon (1.5.0-1) UNRELEASED; urgency=medium
+
+ * Team Upload.
+ * New upstream version 1.5.0 (Closes: #996541)
+
+ -- Nilesh Patra <nilesh at debian.org> Sun, 19 Dec 2021 22:12:39 +0530
+
racon (1.4.21-1) unstable; urgency=medium
* Fix watchfile to detect new versions on github (routine-update)
=====================================
debian/patches/make-compatible-with-old-threadpool.patch
=====================================
@@ -0,0 +1,22 @@
+--- a/src/cuda/cudapolisher.cpp
++++ b/src/cuda/cudapolisher.cpp
+@@ -360,7 +360,7 @@
+ {
+ thread_failed_windows.emplace_back(thread_pool_->Submit(
+ [&](uint64_t j) -> bool {
+- auto it = thread_pool_->thread_map().find(std::this_thread::get_id());
++ auto it = thread_pool_->thread_ids().find(std::this_thread::get_id());
+ return window_consensus_status_.at(j) = windows_[j]->generate_consensus(
+ alignment_engines_[it->second], trim_);
+ }, i));
+--- a/src/polisher.cpp
++++ b/src/polisher.cpp
+@@ -495,7 +495,7 @@
+ for (uint64_t i = 0; i < windows_.size(); ++i) {
+ thread_futures.emplace_back(thread_pool_->Submit(
+ [&](uint64_t j) -> bool {
+- auto it = thread_pool_->thread_map().find(std::this_thread::get_id()); // NOLINT
++ auto it = thread_pool_->thread_ids().find(std::this_thread::get_id()); // NOLINT
+ return windows_[j]->generate_consensus(
+ alignment_engines_[it->second], trim_);
+ }, i));
=====================================
debian/patches/py3
=====================================
@@ -1,8 +1,8 @@
From: Michael R. Crusoe <crusoe at debian.org>
Subject: Mark script as being Python version 3
Forwarded: not-needed
---- racon.orig/scripts/racon_wrapper.py
-+++ racon/scripts/racon_wrapper.py
+--- a/scripts/racon_wrapper.py
++++ b/scripts/racon_wrapper.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
=====================================
debian/patches/remove_buildpath
=====================================
@@ -2,9 +2,9 @@ From: Michael R. Crusoe <michael.crusoe>
Subject: remove unnecessary __FILE__ reference
It reduces the reproduciblilty of the build
---- racon.orig/src/polisher.cpp
-+++ racon/src/polisher.cpp
-@@ -148,8 +148,7 @@
+--- a/src/polisher.cpp
++++ b/src/polisher.cpp
+@@ -146,8 +146,7 @@
#else
fprintf(stderr, "[racon::createPolisher] error: "
"Attemping to use CUDA when CUDA support is not available.\n"
@@ -14,11 +14,3 @@ It reduces the reproduciblilty of the build
exit(1);
#endif
}
---- racon.orig/test/racon_test_config.h.in
-+++ racon/test/racon_test_config.h.in
-@@ -6,4 +6,4 @@
-
- #include <string>
-
--const std::string racon_test_data_path = "@racon_test_data_path@";
-+const std::string racon_test_data_path = "./data/";
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
use_debian_packaged_libs.patch
remove_buildpath
py3
+make-compatible-with-old-threadpool.patch
=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
@@ -1,63 +1,136 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: 2021-01-19
-Description: Use Debian packaged libraries
-Forwarded: not-needed
---- racon.orig/CMakeLists.txt
-+++ racon/CMakeLists.txt
-@@ -47,18 +47,6 @@
- # Add version information to bibary.
- target_compile_definitions(racon PRIVATE RACON_VERSION="v${racon_version}")
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -23,110 +23,8 @@
+ option(racon_build_wrapper "Build wrapper" OFF)
+ option(racon_enable_cuda "Build with NVIDIA CUDA support" OFF)
+
+-find_package(bioparser 3.0.15 QUIET)
+-if (NOT bioparser_FOUND)
+- FetchContent_Declare(
+- bioparser
+- GIT_REPOSITORY https://github.com/rvaser/bioparser
+- GIT_TAG 3.0.15)
+-
+- FetchContent_GetProperties(bioparser)
+- if (NOT bioparser_POPULATED)
+- FetchContent_Populate(bioparser)
+- add_subdirectory(
+- ${bioparser_SOURCE_DIR}
+- ${bioparser_BINARY_DIR}
+- EXCLUDE_FROM_ALL)
+- endif ()
+-endif ()
+-
+-find_package(edlib 1.2.7 QUIET)
+-if (NOT edlib_FOUND)
+- FetchContent_Declare(
+- edlib
+- GIT_REPOSITORY https://github.com/martinsos/edlib
+- GIT_TAG v1.2.7)
+-
+- FetchContent_GetProperties(edlib)
+- if (NOT edlib_POPULATED)
+- FetchContent_Populate(edlib)
+- add_subdirectory(
+- ${edlib_SOURCE_DIR}
+- ${edlib_BINARY_DIR}
+- EXCLUDE_FROM_ALL)
+- endif ()
+-endif ()
+-
+-find_package(spoa 4.0.8 QUIET)
+-if (NOT spoa_FOUND)
+- FetchContent_Declare(
+- spoa
+- GIT_REPOSITORY https://github.com/rvaser/spoa
+- GIT_TAG 4.0.8)
+-
+- FetchContent_GetProperties(spoa)
+- if (NOT spoa_POPULATED)
+- FetchContent_Populate(spoa)
+- add_subdirectory(
+- ${spoa_SOURCE_DIR}
+- ${spoa_BINARY_DIR}
+- EXCLUDE_FROM_ALL)
+- endif ()
+-endif ()
+-
+-find_package(thread_pool 4.0.0 QUIET)
+-if (NOT thread_pool_FOUND)
+- FetchContent_Declare(
+- thread_pool
+- GIT_REPOSITORY https://github.com/rvaser/thread_pool
+- GIT_TAG 4.0.0)
+-
+- FetchContent_GetProperties(thread_pool)
+- if (NOT thread_pool_POPULATED)
+- FetchContent_Populate(thread_pool)
+- add_subdirectory(
+- ${thread_pool_SOURCE_DIR}
+- ${thread_pool_BINARY_DIR}
+- EXCLUDE_FROM_ALL)
+- endif ()
+-endif ()
+-
+ if (racon_build_tests)
+ find_package(GTest 1.10.0 QUIET)
+- if (NOT GTest_FOUND)
+- 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 ()
+-
+-if (racon_build_wrapper)
+- find_package(rampler 2.0.0 QUIET)
+- if (NOT rampler_FOUND)
+- FetchContent_Declare(
+- rampler
+- GIT_REPOSITORY https://github.com/rvaser/rampler
+- GIT_TAG 2.0.0)
+-
+- FetchContent_GetProperties(rampler)
+- if (NOT rampler_POPULATED)
+- FetchContent_Populate(rampler)
+- add_subdirectory(
+- ${rampler_SOURCE_DIR}
+- ${rampler_BINARY_DIR})
+- endif ()
+- endif ()
+ endif ()
--if (NOT TARGET bioparser)
-- add_subdirectory(vendor/spoa/vendor/bioparser EXCLUDE_FROM_ALL)
--endif()
--if (NOT TARGET spoa)
-- add_subdirectory(vendor/spoa EXCLUDE_FROM_ALL)
--endif()
--if (NOT TARGET thread_pool)
-- add_subdirectory(vendor/thread_pool EXCLUDE_FROM_ALL)
--endif()
--if (NOT TARGET edlib)
-- add_subdirectory(vendor/edlib EXCLUDE_FROM_ALL)
--endif()
if (racon_enable_cuda)
- if (DEFINED CLARAGENOMICSANALYSIS_SDK_PATH)
- list(APPEND CMAKE_PREFIX_PATH "${CLARAGENOMICSANALYSIS_SDK_PATH}/cmake")
-@@ -88,7 +76,8 @@
- endif()
- endif()
+@@ -195,11 +93,8 @@
+ ${racon_sources})
+ endif ()
--target_link_libraries(racon bioparser spoa thread_pool edlib_static)
-+target_link_libraries(racon spoa edlib z)
+-target_link_libraries(racon
+- bioparser::bioparser
+- edlib::edlib
+- spoa::spoa
+- thread_pool::thread_pool)
++target_link_libraries(racon edlib spoa pthread z)
+set_target_properties(racon PROPERTIES COMPILE_FLAGS -pthread LINK_FLAGS -pthread)
- if (racon_enable_cuda)
- target_link_libraries(racon cudapoa cudaaligner)
- endif()
-@@ -119,7 +108,7 @@
- add_executable(racon_test ${racon_test_sources})
- endif()
-- target_link_libraries(racon_test bioparser spoa thread_pool edlib_static GTest::Main)
-+ target_link_libraries(racon_test spoa edlib GTest::Main z)
- if (racon_enable_cuda)
- target_link_libraries(racon_test cudapoa cudaaligner)
- endif()
-@@ -127,7 +116,7 @@
+ if (racon_enable_cuda)
+ target_link_libraries(racon
+@@ -245,7 +140,7 @@
if (racon_build_wrapper)
- set(racon_path ${PROJECT_BINARY_DIR}/bin/racon)
-- set(rampler_path ${PROJECT_BINARY_DIR}/vendor/rampler/bin/rampler)
-+ set(rampler_path /usr/bin/rampler)
- configure_file(${PROJECT_SOURCE_DIR}/scripts/racon_wrapper.py
- ${PROJECT_BINARY_DIR}/${CMAKE_FILES_DIRECTORY}/racon_wrapper)
- file(COPY ${PROJECT_BINARY_DIR}/${CMAKE_FILES_DIRECTORY}/racon_wrapper
-@@ -135,9 +124,6 @@
- FILE_PERMISSIONS OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE
- WORLD_READ WORLD_EXECUTE)
-
-- if (NOT TARGET rampler)
-- add_subdirectory(vendor/rampler)
-- endif()
- endif()
-
- # Add Debian packaging
+ set(racon_path ${PROJECT_BINARY_DIR}/bin/racon)
+- set(rampler_path ${PROJECT_BINARY_DIR}/_deps/rampler-build/bin/rampler)
++ set(rampler_path /usr/bin/rampler)
+ if (racon_enable_cuda)
+ set(racon_wrapper_enable_cuda True)
+ else ()
=====================================
meson.build
=====================================
@@ -1,13 +1,13 @@
project(
'Racon',
'cpp',
- version : '1.4.13',
+ version : '1.5.0',
default_options : [
'buildtype=release',
'warning_level=3',
'cpp_std=c++11'],
license : 'MIT',
- meson_version : '>= 0.48')
+ meson_version : '>= 0.50.0')
cpp = meson.get_compiler('cpp')
@@ -19,6 +19,7 @@ opt_compile_with_tests = get_option('tests')
racon_warning_flags = []
racon_cpp_flags = []
+racon_macros = ['-DVERSION="' + meson.project_version() + '"']
################
# Dependencies #
@@ -101,7 +102,7 @@ racon_dep = declare_dependency(
link_with: [racon_lib, vendor_lib],
dependencies: [racon_thread_dep, racon_zlib_dep],
version: meson.project_version(),
- compile_args: racon_warning_flags + racon_cpp_flags)
+ compile_args: racon_warning_flags + racon_cpp_flags + racon_macros)
if not meson.is_subproject()
racon_bin = executable(
@@ -111,12 +112,13 @@ if not meson.is_subproject()
dependencies : [racon_thread_dep, racon_zlib_dep],
include_directories : vendor_include_directories + racon_include_directories,
link_with : [racon_lib],
- cpp_args : [racon_warning_flags, racon_cpp_flags])
+ cpp_args : [racon_warning_flags, racon_cpp_flags, racon_macros])
######################
# Tests #
######################
if opt_compile_with_tests
+ racon_test_macros = ['-DTEST_DATA="' + meson.source_root() + '/test/data/"']
if gtest_dep.found()
tests_bin = executable(
'racon_test',
@@ -124,7 +126,7 @@ if not meson.is_subproject()
dependencies : [racon_thread_dep, racon_zlib_dep, gtest_dep],
include_directories : racon_include_directories + vendor_include_directories + racon_test_include_directories,
link_with : [racon_lib, vendor_lib],
- cpp_args : [racon_warning_flags, racon_cpp_flags, racon_test_extra_flags])
+ cpp_args : [racon_warning_flags, racon_cpp_flags, racon_macros, racon_test_extra_flags, racon_test_macros])
endif
endif
=====================================
scripts/racon_wrapper.py
=====================================
@@ -15,7 +15,7 @@ class RaconWrapper:
def __init__(self, sequences, overlaps, target_sequences, split, subsample,
include_unpolished, fragment_correction, window_length, quality_threshold,
- error_threshold, match, mismatch, gap, threads,
+ error_threshold, match, mismatch, gap, threads, cudaaligner_band_width,
cudaaligner_batches, cudapoa_batches, cuda_banded_alignment):
self.sequences = os.path.abspath(sequences)
@@ -35,9 +35,10 @@ class RaconWrapper:
self.mismatch = mismatch
self.gap = gap
self.threads = threads
- # self.cudaaligner_batches = cudaaligner_batches
- # self.cudapoa_batches = cudapoa_batches
- # self.cuda_banded_alignment = cuda_banded_alignment
+ self.cudaaligner_band_width = cudaaligner_band_width
+ self.cudaaligner_batches = cudaaligner_batches
+ self.cudapoa_batches = cudapoa_batches
+ self.cuda_banded_alignment = cuda_banded_alignment
self.work_directory = os.getcwd() + '/racon_work_directory_' + str(time.time())
def __enter__(self):
@@ -119,17 +120,20 @@ class RaconWrapper:
racon_params = [RaconWrapper.__racon]
if (self.include_unpolished == True): racon_params.append('-u')
if (self.fragment_correction == True): racon_params.append('-f')
- # if (self.cuda_banded_alignment == True): racon_params.append('-b')
racon_params.extend(['-w', str(self.window_length),
'-q', str(self.quality_threshold),
'-e', str(self.error_threshold),
'-m', str(self.match),
'-x', str(self.mismatch),
'-g', str(self.gap),
- '-t', str(self.threads),
- # '--cudaaligner-batches', str(self.cudaaligner_batches),
- # '-c', str(self.cudapoa_batches),
- self.subsampled_sequences, self.overlaps, ""])
+ '-t', str(self.threads)])
+ if (@racon_wrapper_enable_cuda@):
+ if (self.cuda_banded_alignment == True): racon_params.append('-b')
+ racon_params.extend([
+ '--cudaaligner-band-width', str(self.cudaaligner_band_width),
+ '--cudaaligner-batches', str(self.cudaaligner_batches),
+ '-c', str(self.cudapoa_batches)])
+ racon_params.extend([self.subsampled_sequences, self.overlaps, ""])
for target_sequences_part in self.split_target_sequences:
eprint('[RaconWrapper::run] processing data with racon')
@@ -187,10 +191,18 @@ if __name__ == '__main__':
mismatching bases''')
parser.add_argument('-g', '--gap', default=-8, help='''gap penalty (must be
negative)''')
- parser.add_argument('-t', '--threads', default=1, help='''number of threads''')
- parser.add_argument('--cudaaligner-batches', default=0, help='''number of batches for CUDA accelerated alignment''')
- parser.add_argument('-c', '--cudapoa-batches', default=0, help='''number of batches for CUDA accelerated polishing''')
- parser.add_argument('-b', '--cuda-banded-alignment', action='store_true', help='''use banding approximation for polishing on GPU. Only applicable when -c is used.''')
+ parser.add_argument('-t', '--threads', default=1, help='''number of
+ threads''')
+ parser.add_argument('--cudaaligner-band-width', default=0, help='''Band
+ width for cuda alignment. Must be >= 0. Non-zero allows user defined
+ band width, whereas 0 implies auto band width determination.''')
+ parser.add_argument('--cudaaligner-batches', default=0, help='''number of
+ batches for CUDA accelerated alignment''')
+ parser.add_argument('-c', '--cudapoa-batches', default=0, help='''number of
+ batches for CUDA accelerated polishing''')
+ parser.add_argument('-b', '--cuda-banded-alignment', action='store_true',
+ help='''use banding approximation for polishing on GPU. Only applicable
+ when -c is used.''')
args = parser.parse_args()
@@ -198,7 +210,8 @@ if __name__ == '__main__':
args.split, args.subsample, args.include_unpolished,
args.fragment_correction, args.window_length, args.quality_threshold,
args.error_threshold, args.match, args.mismatch, args.gap, args.threads,
- args.cudaaligner_batches, args.cudapoa_batches, args.cuda_banded_alignment)
+ args.cudaaligner_band_width, args.cudaaligner_batches,
+ args.cudapoa_batches, args.cuda_banded_alignment)
with racon:
racon.run()
=====================================
src/cuda/cudapolisher.cpp
=====================================
@@ -360,7 +360,7 @@ void CUDAPolisher::polish(std::vector<std::unique_ptr<Sequence>>& dst,
{
thread_failed_windows.emplace_back(thread_pool_->Submit(
[&](uint64_t j) -> bool {
- auto it = thread_pool_->thread_ids().find(std::this_thread::get_id());
+ auto it = thread_pool_->thread_map().find(std::this_thread::get_id());
return window_consensus_status_.at(j) = windows_[j]->generate_consensus(
alignment_engines_[it->second], trim_);
}, i));
=====================================
src/main.cpp
=====================================
@@ -12,11 +12,6 @@
#include "cuda/cudapolisher.hpp"
#endif
-#ifndef RACON_VERSION
-#error "Undefined version for Racon. Please pass version using -DRACON_VERSION macro."
-#endif
-
-static const char* version = RACON_VERSION;
static const int32_t CUDAALIGNER_INPUT_CODE = 10000;
static const int32_t CUDAALIGNER_BAND_WIDTH_INPUT_CODE = 10001;
@@ -105,7 +100,7 @@ int main(int argc, char** argv) {
num_threads = atoi(optarg);
break;
case 'v':
- printf("%s\n", version);
+ printf("%s\n", VERSION);
exit(0);
case 'h':
help();
=====================================
src/polisher.cpp
=====================================
@@ -30,7 +30,7 @@ namespace racon {
constexpr uint32_t kChunkSize = 1024 * 1024 * 1024; // ~ 1GB
template<class T>
-uint64_t shrinkToFit(std::vector<std::unique_ptr<T>>& src, uint64_t begin) {
+void shrinkToFit(std::vector<std::unique_ptr<T>>& src, uint64_t begin) {
uint64_t i = begin;
for (uint64_t j = begin; i < src.size(); ++i) {
@@ -49,11 +49,9 @@ uint64_t shrinkToFit(std::vector<std::unique_ptr<T>>& src, uint64_t begin) {
src[i].swap(src[j]);
}
}
- uint64_t num_deletions = src.size() - i;
if (i < src.size()) {
src.resize(i);
}
- return num_deletions;
}
std::unique_ptr<Polisher> createPolisher(const std::string& sequences_path,
@@ -311,7 +309,7 @@ void Polisher::initialize() {
};
oparser_->Reset();
- uint64_t l = 0, c = 0;
+ uint64_t c = 0;
while (true) {
auto overlaps_chunk = oparser_->Parse(kChunkSize);
if (overlaps_chunk.empty()) {
@@ -322,7 +320,7 @@ void Polisher::initialize() {
std::make_move_iterator(overlaps_chunk.begin()),
std::make_move_iterator(overlaps_chunk.end()));
- c = l;
+ uint64_t l = c;
for (uint64_t i = l; i < overlaps.size(); ++i) {
overlaps[i]->transmute(sequences_, name_to_id, id_to_id);
@@ -340,11 +338,17 @@ void Polisher::initialize() {
}
}
- uint64_t n = shrinkToFit(overlaps, l);
- l = c - n;
+ uint64_t n = 0;
+ for (uint64_t i = l; i < c; ++i) {
+ if (overlaps[i] == nullptr) {
+ ++n;
+ }
+ }
+ c -= n;
+ shrinkToFit(overlaps, l);
}
- remove_invalid_overlaps(l, overlaps.size());
- shrinkToFit(overlaps, l);
+ remove_invalid_overlaps(c, overlaps.size());
+ shrinkToFit(overlaps, c);
for (const auto& it : overlaps) {
if (it->strand()) {
@@ -492,7 +496,7 @@ void Polisher::polish(std::vector<std::unique_ptr<Sequence>>& dst,
for (uint64_t i = 0; i < windows_.size(); ++i) {
thread_futures.emplace_back(thread_pool_->Submit(
[&](uint64_t j) -> bool {
- auto it = thread_pool_->thread_ids().find(std::this_thread::get_id()); // NOLINT
+ auto it = thread_pool_->thread_map().find(std::this_thread::get_id()); // NOLINT
return windows_[j]->generate_consensus(
alignment_engines_[it->second], trim_);
}, i));
=====================================
test/meson.build
=====================================
@@ -8,7 +8,3 @@ racon_test_extra_flags = []
racon_test_config_h_vars = configuration_data()
racon_test_config_h_vars.set('racon_test_data_path', meson.source_root() + '/test/data/')
-racon_test_config_h = configure_file(
- input : files('racon_test_config.h.in'),
- output : 'racon_test_config.h',
- configuration : racon_test_config_h_vars)
=====================================
test/racon_test.cpp
=====================================
@@ -4,8 +4,6 @@
* @brief Racon unit test source file
*/
-#include "racon_test_config.h"
-
#include "sequence.hpp"
#include "polisher.hpp"
@@ -71,23 +69,23 @@ TEST(RaconInitializeTest, SequencesPathExtensionError) {
}
TEST(RaconInitializeTest, OverlapsPathExtensionError) {
- EXPECT_DEATH((racon::createPolisher(racon_test_data_path + "sample_reads.fastq.gz",
+ EXPECT_DEATH((racon::createPolisher(std::string(TEST_DATA) + "sample_reads.fastq.gz",
"", "", racon::PolisherType::kC, 500, 0, 0, 0, 0, 0, 0, 0)),
".racon::createPolisher. error: file has unsupported format extension "
".valid extensions: .mhap, .mhap.gz, .paf, .paf.gz, .sam, .sam.gz.!");
}
TEST(RaconInitializeTest, TargetPathExtensionError) {
- EXPECT_DEATH((racon::createPolisher(racon_test_data_path + "sample_reads.fastq.gz",
- racon_test_data_path + "sample_overlaps.paf.gz", "", racon::PolisherType::kC,
+ EXPECT_DEATH((racon::createPolisher(std::string(TEST_DATA) + "sample_reads.fastq.gz",
+ std::string(TEST_DATA) + "sample_overlaps.paf.gz", "", racon::PolisherType::kC,
500, 0, 0, 0, 0, 0, 0, 0)), ".racon::createPolisher. error: file has "
"unsupported format extension .valid extensions: .fasta, .fasta.gz, .fna, "
".fna.gz, .fa, .fa.gz, .fastq, .fastq.gz, .fq, .fq.gz.!");
}
TEST_F(RaconPolishingTest, ConsensusWithQualities) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_overlaps.paf.gz", racon_test_data_path + "sample_layout.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_overlaps.paf.gz", std::string(TEST_DATA) + "sample_layout.fasta.gz",
racon::PolisherType::kC, 500, 10, 0.3, 5, -4, -8);
initialize();
@@ -99,7 +97,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualities) {
polished_sequences[0]->create_reverse_complement();
auto parser = bioparser::Parser<racon::Sequence>::Create<bioparser::FastaParser>(
- racon_test_data_path + "sample_reference.fasta.gz");
+ std::string(TEST_DATA) + "sample_reference.fasta.gz");
auto reference = parser->Parse(-1);
EXPECT_EQ(reference.size(), 1);
@@ -109,8 +107,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualities) {
}
TEST_F(RaconPolishingTest, ConsensusWithoutQualities) {
- SetUp(racon_test_data_path + "sample_reads.fasta.gz", racon_test_data_path +
- "sample_overlaps.paf.gz", racon_test_data_path + "sample_layout.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fasta.gz", std::string(TEST_DATA) +
+ "sample_overlaps.paf.gz", std::string(TEST_DATA) + "sample_layout.fasta.gz",
racon::PolisherType::kC, 500, 10, 0.3, 5, -4, -8);
initialize();
@@ -122,7 +120,7 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualities) {
polished_sequences[0]->create_reverse_complement();
auto parser = bioparser::Parser<racon::Sequence>::Create<bioparser::FastaParser>(
- racon_test_data_path + "sample_reference.fasta.gz");
+ std::string(TEST_DATA) + "sample_reference.fasta.gz");
auto reference = parser->Parse(-1);
EXPECT_EQ(reference.size(), 1);
@@ -133,8 +131,8 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualities) {
}
TEST_F(RaconPolishingTest, ConsensusWithQualitiesAndAlignments) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_overlaps.sam.gz", racon_test_data_path + "sample_layout.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_overlaps.sam.gz", std::string(TEST_DATA) + "sample_layout.fasta.gz",
racon::PolisherType::kC, 500, 10, 0.3, 5, -4, -8);
initialize();
@@ -146,7 +144,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesAndAlignments) {
polished_sequences[0]->create_reverse_complement();
auto parser = bioparser::Parser<racon::Sequence>::Create<bioparser::FastaParser>(
- racon_test_data_path + "sample_reference.fasta.gz");
+ std::string(TEST_DATA) + "sample_reference.fasta.gz");
auto reference = parser->Parse(-1);
EXPECT_EQ(reference.size(), 1);
@@ -156,8 +154,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesAndAlignments) {
}
TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesAndWithAlignments) {
- SetUp(racon_test_data_path + "sample_reads.fasta.gz", racon_test_data_path +
- "sample_overlaps.sam.gz", racon_test_data_path + "sample_layout.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fasta.gz", std::string(TEST_DATA) +
+ "sample_overlaps.sam.gz", std::string(TEST_DATA) + "sample_layout.fasta.gz",
racon::PolisherType::kC, 500, 10, 0.3, 5, -4, -8);
initialize();
@@ -169,7 +167,7 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesAndWithAlignments) {
polished_sequences[0]->create_reverse_complement();
auto parser = bioparser::Parser<racon::Sequence>::Create<bioparser::FastaParser>(
- racon_test_data_path + "sample_reference.fasta.gz");
+ std::string(TEST_DATA) + "sample_reference.fasta.gz");
auto reference = parser->Parse(-1);
EXPECT_EQ(reference.size(), 1);
@@ -179,8 +177,8 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesAndWithAlignments) {
}
TEST_F(RaconPolishingTest, ConsensusWithQualitiesLargerWindow) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_overlaps.paf.gz", racon_test_data_path + "sample_layout.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_overlaps.paf.gz", std::string(TEST_DATA) + "sample_layout.fasta.gz",
racon::PolisherType::kC, 1000, 10, 0.3, 5, -4, -8);
initialize();
@@ -192,7 +190,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesLargerWindow) {
polished_sequences[0]->create_reverse_complement();
auto parser = bioparser::Parser<racon::Sequence>::Create<bioparser::FastaParser>(
- racon_test_data_path + "sample_reference.fasta.gz");
+ std::string(TEST_DATA) + "sample_reference.fasta.gz");
auto reference = parser->Parse(-1);
EXPECT_EQ(reference.size(), 1);
@@ -202,8 +200,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesLargerWindow) {
}
TEST_F(RaconPolishingTest, ConsensusWithQualitiesEditDistance) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_overlaps.paf.gz", racon_test_data_path + "sample_layout.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_overlaps.paf.gz", std::string(TEST_DATA) + "sample_layout.fasta.gz",
racon::PolisherType::kC, 500, 10, 0.3, 1, -1, -1);
initialize();
@@ -215,7 +213,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesEditDistance) {
polished_sequences[0]->create_reverse_complement();
auto parser = bioparser::Parser<racon::Sequence>::Create<bioparser::FastaParser>(
- racon_test_data_path + "sample_reference.fasta.gz");
+ std::string(TEST_DATA) + "sample_reference.fasta.gz");
auto reference = parser->Parse(-1);
EXPECT_EQ(reference.size(), 1);
@@ -225,8 +223,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesEditDistance) {
}
TEST_F(RaconPolishingTest, FragmentCorrectionWithQualities) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_ava_overlaps.paf.gz", racon_test_data_path + "sample_reads.fastq.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_ava_overlaps.paf.gz", std::string(TEST_DATA) + "sample_reads.fastq.gz",
racon::PolisherType::kC, 500, 10, 0.3, 1, -1, -1);
initialize();
@@ -243,8 +241,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithQualities) {
}
TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesFull) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_ava_overlaps.paf.gz", racon_test_data_path + "sample_reads.fastq.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_ava_overlaps.paf.gz", std::string(TEST_DATA) + "sample_reads.fastq.gz",
racon::PolisherType::kF, 500, 10, 0.3, 1, -1, -1);
initialize();
@@ -261,8 +259,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesFull) {
}
TEST_F(RaconPolishingTest, FragmentCorrectionWithoutQualitiesFull) {
- SetUp(racon_test_data_path + "sample_reads.fasta.gz", racon_test_data_path +
- "sample_ava_overlaps.paf.gz", racon_test_data_path + "sample_reads.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fasta.gz", std::string(TEST_DATA) +
+ "sample_ava_overlaps.paf.gz", std::string(TEST_DATA) + "sample_reads.fasta.gz",
racon::PolisherType::kF, 500, 10, 0.3, 1, -1, -1);
initialize();
@@ -279,8 +277,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithoutQualitiesFull) {
}
TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesFullMhap) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_ava_overlaps.mhap.gz", racon_test_data_path + "sample_reads.fastq.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_ava_overlaps.mhap.gz", std::string(TEST_DATA) + "sample_reads.fastq.gz",
racon::PolisherType::kF, 500, 10, 0.3, 1, -1, -1);
initialize();
@@ -298,8 +296,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesFullMhap) {
#ifdef CUDA_ENABLED
TEST_F(RaconPolishingTest, ConsensusWithQualitiesCUDA) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_overlaps.paf.gz", racon_test_data_path + "sample_layout.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_overlaps.paf.gz", std::string(TEST_DATA) + "sample_layout.fasta.gz",
racon::PolisherType::kC, 500, 10, 0.3, 5, -4, -8, 1);
initialize();
@@ -311,7 +309,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesCUDA) {
polished_sequences[0]->create_reverse_complement();
auto parser = bioparser::Parser<racon::Sequence>::Create<bioparser::FastaParser>(
- racon_test_data_path + "sample_reference.fasta.gz");
+ std::string(TEST_DATA) + "sample_reference.fasta.gz");
auto reference = parser->Parse(-1);
EXPECT_EQ(reference.size(), 1);
@@ -321,8 +319,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesCUDA) {
}
TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesCUDA) {
- SetUp(racon_test_data_path + "sample_reads.fasta.gz", racon_test_data_path +
- "sample_overlaps.paf.gz", racon_test_data_path + "sample_layout.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fasta.gz", std::string(TEST_DATA) +
+ "sample_overlaps.paf.gz", std::string(TEST_DATA) + "sample_layout.fasta.gz",
racon::PolisherType::kC, 500, 10, 0.3, 5, -4, -8, 1);
initialize();
@@ -334,7 +332,7 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesCUDA) {
polished_sequences[0]->create_reverse_complement();
auto parser = bioparser::Parser<racon::Sequence>::Create<bioparser::FastaParser>(
- racon_test_data_path + "sample_reference.fasta.gz");
+ std::string(TEST_DATA) + "sample_reference.fasta.gz");
auto reference = parser->Parse(-1);
EXPECT_EQ(reference.size(), 1);
@@ -344,8 +342,8 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesCUDA) {
}
TEST_F(RaconPolishingTest, ConsensusWithQualitiesAndAlignmentsCUDA) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_overlaps.sam.gz", racon_test_data_path + "sample_layout.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_overlaps.sam.gz", std::string(TEST_DATA) + "sample_layout.fasta.gz",
racon::PolisherType::kC, 500, 10, 0.3, 5, -4, -8, 1);
initialize();
@@ -357,7 +355,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesAndAlignmentsCUDA) {
polished_sequences[0]->create_reverse_complement();
auto parser = bioparser::Parser<racon::Sequence>::Create<bioparser::FastaParser>(
- racon_test_data_path + "sample_reference.fasta.gz");
+ std::string(TEST_DATA) + "sample_reference.fasta.gz");
auto reference = parser->Parse(-1);
EXPECT_EQ(reference.size(), 1);
@@ -367,8 +365,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesAndAlignmentsCUDA) {
}
TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesAndWithAlignmentsCUDA) {
- SetUp(racon_test_data_path + "sample_reads.fasta.gz", racon_test_data_path +
- "sample_overlaps.sam.gz", racon_test_data_path + "sample_layout.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fasta.gz", std::string(TEST_DATA) +
+ "sample_overlaps.sam.gz", std::string(TEST_DATA) + "sample_layout.fasta.gz",
racon::PolisherType::kC, 500, 10, 0.3, 5, -4, -8, 1);
initialize();
@@ -380,7 +378,7 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesAndWithAlignmentsCUDA) {
polished_sequences[0]->create_reverse_complement();
auto parser = bioparser::Parser<racon::Sequence>::Create<bioparser::FastaParser>(
- racon_test_data_path + "sample_reference.fasta.gz");
+ std::string(TEST_DATA) + "sample_reference.fasta.gz");
auto reference = parser->Parse(-1);
EXPECT_EQ(reference.size(), 1);
@@ -390,8 +388,8 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesAndWithAlignmentsCUDA) {
}
TEST_F(RaconPolishingTest, ConsensusWithQualitiesLargerWindowCUDA) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_overlaps.paf.gz", racon_test_data_path + "sample_layout.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_overlaps.paf.gz", std::string(TEST_DATA) + "sample_layout.fasta.gz",
racon::PolisherType::kC, 1000, 10, 0.3, 5, -4, -8, 1);
initialize();
@@ -403,7 +401,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesLargerWindowCUDA) {
polished_sequences[0]->create_reverse_complement();
auto parser = bioparser::Parser<racon::Sequence>::Create<bioparser::FastaParser>(
- racon_test_data_path + "sample_reference.fasta.gz");
+ std::string(TEST_DATA) + "sample_reference.fasta.gz");
auto reference = parser->Parse(-1);
EXPECT_EQ(reference.size(), 1);
@@ -413,8 +411,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesLargerWindowCUDA) {
}
TEST_F(RaconPolishingTest, ConsensusWithQualitiesEditDistanceCUDA) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_overlaps.paf.gz", racon_test_data_path + "sample_layout.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_overlaps.paf.gz", std::string(TEST_DATA) + "sample_layout.fasta.gz",
racon::PolisherType::kC, 500, 10, 0.3, 1, -1, -1, 1);
initialize();
@@ -426,7 +424,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesEditDistanceCUDA) {
polished_sequences[0]->create_reverse_complement();
auto parser = bioparser::Parser<racon::Sequence>::Create<bioparser::FastaParser>(
- racon_test_data_path + "sample_reference.fasta.gz");
+ std::string(TEST_DATA) + "sample_reference.fasta.gz");
auto reference = parser->Parse(-1);
EXPECT_EQ(reference.size(), 1);
@@ -436,8 +434,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesEditDistanceCUDA) {
}
TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesCUDA) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_ava_overlaps.paf.gz", racon_test_data_path + "sample_reads.fastq.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_ava_overlaps.paf.gz", std::string(TEST_DATA) + "sample_reads.fastq.gz",
racon::PolisherType::kC, 500, 10, 0.3, 1, -1, -1, 1);
initialize();
@@ -454,8 +452,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesCUDA) {
}
TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesFullCUDA) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_ava_overlaps.paf.gz", racon_test_data_path + "sample_reads.fastq.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_ava_overlaps.paf.gz", std::string(TEST_DATA) + "sample_reads.fastq.gz",
racon::PolisherType::kF, 500, 10, 0.3, 1, -1, -1, 1);
initialize();
@@ -472,8 +470,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesFullCUDA) {
}
TEST_F(RaconPolishingTest, FragmentCorrectionWithoutQualitiesFullCUDA) {
- SetUp(racon_test_data_path + "sample_reads.fasta.gz", racon_test_data_path +
- "sample_ava_overlaps.paf.gz", racon_test_data_path + "sample_reads.fasta.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fasta.gz", std::string(TEST_DATA) +
+ "sample_ava_overlaps.paf.gz", std::string(TEST_DATA) + "sample_reads.fasta.gz",
racon::PolisherType::kF, 500, 10, 0.3, 1, -1, -1, 1);
initialize();
@@ -490,8 +488,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithoutQualitiesFullCUDA) {
}
TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesFullMhapCUDA) {
- SetUp(racon_test_data_path + "sample_reads.fastq.gz", racon_test_data_path +
- "sample_ava_overlaps.mhap.gz", racon_test_data_path + "sample_reads.fastq.gz",
+ SetUp(std::string(TEST_DATA) + "sample_reads.fastq.gz", std::string(TEST_DATA) +
+ "sample_ava_overlaps.mhap.gz", std::string(TEST_DATA) + "sample_reads.fastq.gz",
racon::PolisherType::kF, 500, 10, 0.3, 1, -1, -1, 1);
initialize();
=====================================
test/racon_test_config.h.in deleted
=====================================
@@ -1,9 +0,0 @@
-/*!
- * @file racon_test_config.h.in
- *
- * @brief Racon test configuration file
- */
-
-#include <string>
-
-const std::string racon_test_data_path = "@racon_test_data_path@";
=====================================
vendor/meson.build
=====================================
@@ -4,9 +4,9 @@ vendor_cpp_sources = files([
'rampler/src/sampler.cpp',
'spoa/src/alignment_engine.cpp',
- 'spoa/src/dispatcher.cpp',
'spoa/src/graph.cpp',
'spoa/src/simd_alignment_engine_dispatch.cpp',
+ 'spoa/src/simd_alignment_engine_dispatcher.cpp',
'spoa/src/sisd_alignment_engine.cpp',
])
View it on GitLab: https://salsa.debian.org/med-team/racon/-/compare/863a708321972722822b0ce4ddecfd6499dcb31c...ff3662b49dc15dbd04d6a14d8ad127dc3e470bbe
--
View it on GitLab: https://salsa.debian.org/med-team/racon/-/compare/863a708321972722822b0ce4ddecfd6499dcb31c...ff3662b49dc15dbd04d6a14d8ad127dc3e470bbe
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