fix boost link issue

format

.github/workflows/linux.yml

@@ -5,9 +5,11 @@ on:
     branches:
       - main
       - release*
+      - master
   pull_request:
     branches:
       - main
+      - master
       - release*
 
 env:

README.md

@@ -5,13 +5,13 @@
 [![License](https://img.shields.io/github/license/ylab-hi/BINARY)](https://github.com/cauliyang/boss/blob/main/LICENSE)
 ![compiler](https://img.shields.io/badge/Compiler-GCC10%20%7C%20GCC11%20%7C%20GCC12-green)
 
-# BioinfOrmaticS toolboxeS aka BOSS
+# **B**ioinf**O**rmatic**S** toolboxe**S** aka **BOSS**
 
 ## Current Tools
 
 | Tool                    | Description                         | Status                                                         |
 |-------------------------|-------------------------------------|----------------------------------------------------------------|
-| [boss-fqsp](#boss-fqsp) | Fastq Splitter for Paried End Reads | ![boss-fqsp](https://img.shields.io/badge/Version-1.0.0-green) |
+| [boss-fqsp](#boss-fqsp) | Fastq Splitter for Paired End Reads | ![boss-fqsp](https://img.shields.io/badge/Version-1.0.0-green) |
 
 ## Usage
 

include/CMakeLists.txt

@@ -18,9 +18,12 @@ if(PROJECT_SOURCE_DIR STREQUAL PROJECT_BINARY_DIR)
   )
 endif()
 
+option(BOSS_HAS_BOOST "Do not download Boost" OFF)
+
 message(STATUS "Started CMake for  ${PROJECT_NAME} v${PROJECT_VERSION}...")
 message(STATUS "Compiler name: ${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILER_VERSION}")
 message(STATUS "Cmake Binary path: ${CMAKE_BINARY_DIR}")
+message(STATUS "BOSS has boost: ${BOSS_HAS_BOOST}")
 
 # ---- Add dependencies via CPM ----
 # see https://github.com/TheLartians/CPM.cmake for more info
@@ -30,14 +33,8 @@ include(../cmake/CPM.cmake)
 # PackageProject.cmake will be used to make our target installable
 CPMAddPackage("gh:TheLartians/[email protected]")
 
-CPMAddPackage(
-  NAME spdlog
-  GITHUB_REPOSITORY gabime/spdlog
-  VERSION 1.10.0
-  OPTIONS "SPDLOG_INSTALL YES"
-)
-
 find_package(Boost REQUIRED)
+
 # ---- Add source files ----
 
 # Note: globbing sources is considered bad practice as CMake's generators may not detect new files
@@ -56,7 +53,7 @@ set_target_properties(${PROJECT_NAME} PROPERTIES CXX_STANDARD 20)
 target_compile_options(${PROJECT_NAME} PUBLIC "$<$<COMPILE_LANG_AND_ID:CXX,MSVC>:/permissive->")
 
 # Link dependencies
-target_link_libraries(${PROJECT_NAME} PUBLIC spdlog::spdlog Boost::boost)
+target_link_libraries(${PROJECT_NAME} PUBLIC spdlog::spdlog Boost::boost boost_iostreams)
 
 target_include_directories(
   ${PROJECT_NAME} PUBLIC $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/../include>

include/boss/fq_utils.hpp

@@ -1,13 +1,22 @@
 #ifndef FQ_UTILS_H
 #define FQ_UTILS_H
 
+#include <spdlog/spdlog.h>
+
 #include <boost/iostreams/categories.hpp>  // input_filter_tag
+#include <boost/iostreams/copy.hpp>
+#include <boost/iostreams/device/file.hpp>
+#include <boost/iostreams/filter/gzip.hpp>
+#include <boost/iostreams/filtering_stream.hpp>
 #include <boost/iostreams/operations.hpp>  // get, put, WOULD_BLOCK
 #include <cstdio>                          // EOF.
 #include <filesystem>
 
-namespace boss {
+namespace boss::fqsp {
+
   namespace fs = std::filesystem;
+  enum class FqDirection;
+  class fq_filter;
 
   enum class FqDirection { Forward, Reverse };
 
@@ -62,10 +71,56 @@ namespace boss {
     int saved_line_count_{0};
   };
 
-  //--------------Definitions of helper functions for splitting ncbi fq files----//
+  namespace details {
+
+    struct txt_tag {};
+    struct gzip_tag : txt_tag {};
+    struct bzip2_tag : txt_tag {};
+
+    txt_tag format_category(std::string_view path) {
+      if (path.ends_with(".gz")) {
+        return gzip_tag{};
+      } else if (path.ends_with(".bz2")) {
+        return bzip2_tag{};
+      } else {
+        return txt_tag{};
+      }
+    }
+
+    //----------------------------Define helper functions---------------------------//
+    void split_fq_impl(const fs::path& input, FqDirection direction, gzip_tag) {
+      boost::iostreams::filtering_istream in;
+      in.push(fq_filter(direction));
+      in.push(boost::iostreams::gzip_decompressor());
+      in.push(boost::iostreams::file_source(input, std::ios_base::in | std::ios_base::binary));
+
+      std::ofstream out{fmt::format("{}{}{}", input.stem().string(),
+                                    direction == FqDirection::Forward ? "1" : "2",
+                                    input.extension().string())};
+      boost::iostreams::copy(in, out);
+      out.close();
+    }
+
+    void split_fq_impl(const fs::path& input, FqDirection direction, txt_tag) {
+      boost::iostreams::filtering_istream in;
+      in.push(fq_filter(direction));
+      in.push(boost::iostreams::file_source(input, std::ios_base::in));
+      std::ofstream out{fmt::format("{}{}{}", input.stem().string(),
+                                    direction == FqDirection::Forward ? "1" : "2",
+                                    input.extension().string())};
+      boost::iostreams::copy(in, out);
+      out.close();
+    }
+
+  }  // namespace details
+
+  //--------------Definitions of functions for splitting ncbi fq files----//
 
-  [[nodiscard]] bool is_gzip(std::string_view path);
+  void split_fq(const fs::path& input) {
+    details::split_fq_impl(input, FqDirection::Forward, details::format_category(input.string()));
+    details::split_fq_impl(input, FqDirection::Reverse, details::format_category(input.string()));
+  }
 
-}  // namespace boss
+}  // namespace boss::fqsp
 
 #endif  // FQ_UTILS_H

source/fq_utils.cpp

@@ -1,5 +1,4 @@
+
 #include <boss/fq_utils.hpp>
-namespace boss {
 
-  bool is_gzip(std::string_view path) { return path.ends_with(".gz"); }
-}  // namespace boss
+namespace boss::fqsp {}  // namespace boss::fqsp

standalone/CMakeLists.txt

@@ -11,40 +11,37 @@ include(../cmake/tools.cmake)
 include(../cmake/CPM.cmake)
 
 CPMAddPackage(
-        GITHUB_REPOSITORY ylab-hi/BINARY
-        VERSION 1.1.0
-        OPTIONS "BINARY_BUILD_STANDALONE NO"  "BINARY_BUILD_TESTS NO"
+  GITHUB_REPOSITORY ylab-hi/BINARY
+  VERSION 1.1.0
+  OPTIONS "BINARY_BUILD_STANDALONE NO" "BINARY_BUILD_TESTS NO"
 )
 
-
 CPMAddPackage(
-        GITHUB_REPOSITORY jarro2783/cxxopts
-        VERSION 3.0.0
-        OPTIONS "CXXOPTS_BUILD_EXAMPLES NO" "CXXOPTS_BUILD_TESTS NO" "CXXOPTS_ENABLE_INSTALL YES"
+  GITHUB_REPOSITORY jarro2783/cxxopts
+  VERSION 3.0.0
+  OPTIONS "CXXOPTS_BUILD_EXAMPLES NO" "CXXOPTS_BUILD_TESTS NO" "CXXOPTS_ENABLE_INSTALL YES"
 )
 
-
 CPMAddPackage(NAME BOSS SOURCE_DIR ${CMAKE_CURRENT_LIST_DIR}/../include)
 
 # ---- Create standalone executable ----
 
-
 function(add_standalone targetName)
-    message(STATUS "Adding standalone ${targetName}")
-    file(GLOB ${targetName}_source CONFIGURE_DEPENDS
-            ${CMAKE_CURRENT_LIST_DIR}/${targetName}/source/*.cpp
-            )
-    add_executable(${targetName} ${${targetName}_source})
-    target_compile_features(${targetName} PRIVATE cxx_std_20)
-    target_link_libraries(${targetName} PRIVATE boss::boss binary cxxopts stdc++fs)
-    target_include_directories(
-            ${targetName} PRIVATE ${CMAKE_CURRENT_LIST_DIR}/include
-            ${CMAKE_CURRENT_LIST_DIR}/${targetName}/include
-    )
-    target_compile_options(${targetName} PRIVATE -Wall -Wextra -Wnon-virtual-dtor -pedantic -Werror)
-    set_target_properties(${targetName} PROPERTIES CXX_EXTENSIONS OFF OUTPUT_NAME boss-${targetName})
+  message(STATUS "Adding standalone ${targetName}")
+  file(GLOB ${targetName}_source CONFIGURE_DEPENDS
+       ${CMAKE_CURRENT_LIST_DIR}/${targetName}/source/*.cpp
+  )
+  add_executable(${targetName} ${${targetName}_source})
+  target_compile_features(${targetName} PRIVATE cxx_std_20)
+  target_link_libraries(${targetName} PRIVATE boss::boss binary cxxopts stdc++fs)
+  target_include_directories(
+    ${targetName} PRIVATE ${CMAKE_CURRENT_LIST_DIR}/include
+                          ${CMAKE_CURRENT_LIST_DIR}/${targetName}/include
+  )
+  target_compile_options(${targetName} PRIVATE -Wall -Wextra -Wnon-virtual-dtor -pedantic -Werror)
+  set_target_properties(${targetName} PROPERTIES CXX_EXTENSIONS OFF OUTPUT_NAME boss-${targetName})
 endfunction()
 
-#file(GLOB sources CONFIGURE_DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/source/*.cpp)
+# file(GLOB sources CONFIGURE_DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/source/*.cpp)
 
-add_standalone(fqsp)
+add_standalone(fqsp)

standalone/fqsp/source/main.cpp

@@ -46,8 +46,10 @@ auto main(int argc, char** argv) -> int {
       std::exit(1);
     }
 
+    boss::fqsp::split_fq(fs::path(input));
+
   } catch (const cxxopts::OptionException& e) {
-    spdlog::error("{}",  e.what());
+    spdlog::error("{}", e.what());
     std::exit(1);
   }