New upstream version 1.4.10 (46027c68) · Commits · Debian Med / racon

.gitmodules

+0 −3

Original line number	Diff line number	Diff line
		@@ -16,9 +16,6 @@
		[submodule "vendor/rampler"]
		path = vendor/rampler
		url = https://github.com/rvaser/rampler
		[submodule "vendor/logger"]
		path = vendor/logger
		url = https://github.com/rvaser/logger
		[submodule "vendor/ClaraGenomicsAnalysis"]
		path = vendor/ClaraGenomicsAnalysis
		url = https://github.com/clara-genomics/ClaraGenomicsAnalysis

CMakeLists.txt

+5 −6

Original line number	Diff line number	Diff line
		cmake_minimum_required(VERSION 3.2)
		project(racon)
		set(racon_version 1.4.7)
		set(racon_version 1.4.10)

		set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
		set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
		@@ -30,6 +30,7 @@ include_directories(${PROJECT_SOURCE_DIR}/src)

		set(racon_sources
		src/main.cpp
		src/logger.cpp
		src/polisher.cpp
		src/overlap.cpp
		src/sequence.cpp
		@@ -58,9 +59,6 @@ endif()
		if (NOT TARGET edlib)
		add_subdirectory(vendor/edlib EXCLUDE_FROM_ALL)
		endif()
		if (NOT TARGET logger)
		add_subdirectory(vendor/logger EXCLUDE_FROM_ALL)
		endif()
		if (racon_enable_cuda)
		if (DEFINED CLARAGENOMICSANALYSIS_SDK_PATH)
		list(APPEND CMAKE_PREFIX_PATH "${CLARAGENOMICSANALYSIS_SDK_PATH}/cmake")
		@@ -90,7 +88,7 @@ if (racon_enable_cuda)
		endif()
		endif()

		target_link_libraries(racon bioparser spoa thread_pool edlib_static logger)
		target_link_libraries(racon bioparser spoa thread_pool edlib_static)
		if (racon_enable_cuda)
		target_link_libraries(racon cudapoa cudaaligner)
		endif()
		@@ -106,6 +104,7 @@ if (racon_build_tests)

		set(racon_test_sources
		test/racon_test.cpp
		src/logger.cpp
		src/polisher.cpp
		src/overlap.cpp
		src/sequence.cpp
		@@ -123,7 +122,7 @@ if (racon_build_tests)
		add_subdirectory(vendor/googletest/googletest EXCLUDE_FROM_ALL)
		endif()

		target_link_libraries(racon_test bioparser spoa thread_pool edlib_static logger gtest_main)
		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()

src/cuda/cudapolisher.cpp

+1 −1

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		@@ -10,11 +10,11 @@
		#include <cuda_profiler_api.h>

		#include "sequence.hpp"
		#include "logger.hpp"
		#include "cudapolisher.hpp"
		#include <claragenomics/utils/cudautils.hpp>

		#include "bioparser/bioparser.hpp"
		#include "logger/logger.hpp"

		namespace racon {

src/logger.cpp

0 → 100644

+56 −0

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		/*!
		* @file logger.cpp
		*
		* @brief Logger source file
		*/

		#include <iostream>

		#include "logger.hpp"

		namespace racon {

		Logger::Logger()
		: time_(0.), bar_(0), time_point_() {
		}

		Logger::~Logger() {
		}

		void Logger::log() {
		auto now = std::chrono::steady_clock::now();
		if (time_point_ != std::chrono::time_point<std::chrono::steady_clock>()) {
		time_ += std::chrono::duration_cast<std::chrono::duration<double>>(now - time_point_).count();
		}
		time_point_ = now;
		}

		void Logger::log(const std::string& msg) const {
		std::cerr << msg << " " << std::fixed
		<< std::chrono::duration_cast<std::chrono::duration<double>>(std::chrono::steady_clock::now() - time_point_).count()
		<< " s" << std::endl;
		}

		void Logger::bar(const std::string& msg) {
		++bar_;
		std::string progress_bar = "[" + std::string(bar_, '=') + (bar_ == 20 ? "" : ">" + std::string(19 - bar_, ' ')) + "]";

		std::cerr << msg << " " << progress_bar << " " << std::fixed
		<< std::chrono::duration_cast<std::chrono::duration<double>>(std::chrono::steady_clock::now() - time_point_).count()
		<< " s";

		bar_ %= 20;
		if (bar_ == 0) {
		std::cerr << std::endl;
		} else {
		std::cerr << "\r";
		}
		}

		void Logger::total(const std::string& msg) const {
		std::cerr << msg << " " << std::fixed
		<< time_ + std::chrono::duration_cast<std::chrono::duration<double>>(std::chrono::steady_clock::now() - time_point_).count()
		<< " s" << std::endl;
		}

		}

src/logger.hpp

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		/*!
		* @file logger.hpp
		*
		* @brief Logger header file
		*/

		#pragma once

		#include <cstdint>
		#include <chrono>
		#include <string>

		namespace racon {

		static const std::string version = "v1.0.0";

		class Logger {
		public:
		Logger();

		Logger(const Logger&) = default;
		Logger& operator=(const Logger&) = default;

		Logger(Logger&&) = default;
		Logger& operator=(Logger&&) = default;

		~Logger();

		/*!
		* @brief Resets the time point
		*/
		void log();

		/*!
		* @brief Prints the elapsed time from last time point to stderr
		*/
		void log(const std::string& msg) const;

		/*!
		* @brief Prints a progress bar and the elapsed time from last time to
		* stderr (the progress bar resets after 20 calls)
		*/
		void bar(const std::string& msg);

		/*!
		* @brief Prints the total elapsed time from the first log() call
		*/
		void total(const std::string& msg) const;

		private:
		double time_;
		std::uint32_t bar_;
		std::chrono::time_point<std::chrono::steady_clock> time_point_;
		};

		}