Commit bd4699a0 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.12.0+dfsg

parent b8057c0d

.vscode/c_cpp_properties.json

0 → 100644
+73 −0
Original line number Diff line number Diff line 
{

    "configurations": [

        {

            "name": "Mac",

            "includePath": [

                "/usr/local/include",

                "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1",

                "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/9.0.0/include",

                "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include",

                "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include",

                "${workspaceRoot}",

                "${workspaceRoot}/include"

            ],

            "defines": [],

            "intelliSenseMode": "clang-x64",

            "browse": {

                "path": [

                    "/usr/local/include",

                    "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1",

                    "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/9.0.0/include",

                    "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include",

                    "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include",

                    "${workspaceRoot}"

                ],

                "limitSymbolsToIncludedHeaders": true,

                "databaseFilename": ""

            },

            "macFrameworkPath": [

                "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/System/Library/Frameworks"

            ]

        },

        {

            "name": "Linux",

            "includePath": [

                "/usr/include",

                "/usr/local/include",

                "${workspaceRoot}"

            ],

            "defines": [],

            "intelliSenseMode": "clang-x64",

            "browse": {

                "path": [

                    "/usr/include",

                    "/usr/local/include",

                    "${workspaceRoot}"

                ],

                "limitSymbolsToIncludedHeaders": true,

                "databaseFilename": ""

            }

        },

        {

            "name": "Win32",

            "includePath": [

                "C:/Program Files (x86)/Microsoft Visual Studio 14.0/VC/include",

                "${workspaceRoot}"

            ],

            "defines": [

                "_DEBUG",

                "UNICODE"

            ],

            "intelliSenseMode": "msvc-x64",

            "browse": {

                "path": [

                    "C:/Program Files (x86)/Microsoft Visual Studio 14.0/VC/include/*",

                    "${workspaceRoot}"

                ],

                "limitSymbolsToIncludedHeaders": true,

                "databaseFilename": ""

            }

        }

    ],

    "version": 3

}
 
 No newline at end of file

CMakeLists.txt

+23 −44
Original line number Diff line number Diff line 
cmake_minimum_required (VERSION 2.8)

cmake_minimum_required (VERSION 3.1)



enable_testing()



project (RapMap)



set(CPACK_PACKAGE_VERSION "0.5.0")

set(CPACK_PACKAGE_VERSION "0.6.0")

SET(CPACK_PACKAGE_VERSION_MAJOR "0")

set(CPACK_PACKAGE_VERSION_MINOR "5")

set(CPACK_PACKAGE_VERSION_MINOR "6")

set(CPACK_PACKAGE_VERSION_PATCH "0")

set(PROJECT_VERSION ${CPACK_PACKAGE_VERSION})

set(CPACK_GENERATOR "TGZ")

set(CPACK_SOURCE_GENERATOR "TGZ")

set(CPACK_PACKAGE_VENDOR "Stony Brook University")

set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "RapMap - Wicked-fast qasi-mapping")

set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "RapMap - Wicked-fast quasi-mapping")

set(CPACK_PACKAGE_NAME

  "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")

set(CPACK_SOURCE_PACKAGE_FILE_NAME
@@ -46,10 +46,10 @@ endif() 
if (QUIET_BUILD)

  set(WALL "")

else()

  set(WALL "-Wall")

  set(WALL "-Wall -Wno-unused-function -Wno-unused-local-typedef")

endif()



set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM ${WALL} -std=c++11")

set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM ${WALL} -std=c++14")



set(CMAKE_THREAD_PREFER_PTHREAD TRUE)

find_package(Threads REQUIRED)
@@ -89,11 +89,11 @@ if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "GNU") 
    execute_process(

        COMMAND ${CMAKE_CXX_COMPILER} -dumpversion OUTPUT_VARIABLE GCC_VERSION)

    # If we're on OSX

    if (APPLE AND NOT (GCC_VERSION VERSION_GREATER 4.8.2 OR GCC_VERSION VERSION_EQUAL 4.8.2))

    if (APPLE AND NOT (GCC_VERSION VERSION_GREATER 5.2 OR GCC_VERSION VERSION_EQUAL 5.2))

        message(FATAL_ERROR "When building under OSX, ${PROJECT_NAME} requires "

                            "either clang or g++ >= 4.8.2")

    elseif (NOT (GCC_VERSION VERSION_GREATER 4.7 OR GCC_VERSION VERSION_EQUAL 4.7))

        message(FATAL_ERROR "${PROJECT_NAME} requires g++ 4.7 or greater.")

                            "either clang or g++ >= 5.2")

    elseif (NOT (GCC_VERSION VERSION_GREATER 5.2 OR GCC_VERSION VERSION_EQUAL 5.2))

        message(FATAL_ERROR "${PROJECT_NAME} requires g++ 5.2 or greater.")

    endif ()



    set (GCC TRUE)
@@ -134,7 +134,7 @@ elseif ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang") 
        set (PTHREAD_LIB "pthread")

    endif()

else ()

    message(FATAL_ERROR "Your C++ compiler does not support C++11.")

    message(FATAL_ERROR "Your C++ compiler does not support C++14.")

endif ()



include(ExternalProject)
@@ -209,50 +209,29 @@ if (NOT CEREAL_FOUND) 


endif()





if (NOT JELLYFISH_ROOT)

	set(JELLYFISH_ROOT ${GAT_SOURCE_DIR}/external/install)

endif()



find_package(Jellyfish 2.2.6)



if (NOT JELLYFISH_FOUND)

message("Build system will fetch and build Jellyfish")

message("==================================================================")

ExternalProject_Add(libjellyfish

    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external

    DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.6/jellyfish-2.2.6.tar.gz -o jellyfish-2.2.6.tgz &&

    	rm -fr jellyfish-2.2.6 &&

     	tar -xzvf jellyfish-2.2.6.tgz

    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6

    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install

    CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6/configure --enable-shared=no --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}

    BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}

    BUILD_IN_SOURCE 1

    INSTALL_COMMAND make install

)

endif()



set (FAST_MALLOC_LIB "")

set (HAVE_FAST_MALLOC FALSE)





# See if we have Jemalloc

find_package(Jemalloc)

if (Jemalloc_FOUND)

  ##

  # Don't be so stringent about the version yet

  ##

  #if (NOT (${JEMALLOC_VERSION} VERSION_LESS 5.1.0))

    message("Found Jemalloc library --- using this memory allocator")

    set (FAST_MALLOC_LIB ${JEMALLOC_LIBRARIES})

    set (HAVE_FAST_MALLOC TRUE)

  #else()

  #  message("Fond Jemalloc version ${JEMALLOC_VERSION}, but require >= 5.1.0. Downloading newer version")

  #endif()

endif()



if (NOT HAVE_FAST_MALLOC)

    # See if we have Tcmalloc

    find_package(Tcmalloc)

    if (Tcmalloc_FOUND)

        message("Fount TCMalloc library --- using this memory allocator")

        set (TCMALLOC_LIB ${Tcmalloc_LIBRARIES})

        set (FAST_MALLOC_LIB ${TCMALLOC_LIB})

        set (HAVE_FAST_MALLOC TRUE)

    endif()

if(CONDA_BUILD)

  set (JEMALLOC_FLAGS "CC=${CMAKE_C_COMPILER} CFLAGS=-fPIC CPPFLAGS=-fPIC")

else ()

  set (JEMALLOC_FLAGS "CC=${CMAKE_C_COMPILER}")

endif()



if (NOT HAVE_FAST_MALLOC)

cmake/Modules/FindJemalloc.cmake

+20 −13
Original line number Diff line number Diff line
@@ -28,19 +28,26 @@ find_library(JEMALLOC_LIBRARY NAMES jemalloc libjemalloc 
    ${PC_JEMALLOC_LIBRARY_DIRS}

  PATH_SUFFIXES lib lib64)



set(JEMALLOC_LIBRARIES ${JEMALLOC_LIBRARY})

set(JEMALLOC_INCLUDE_DIRS ${JEMALLOC_INCLUDE_DIR})

if(JEMALLOC_INCLUDE_DIR)

  set(_version_regex "^#define[ \t]+JEMALLOC_VERSION[ \t]+\"([^\"]+)\".*")

  file(STRINGS "${JEMALLOC_INCLUDE_DIR}/jemalloc/jemalloc.h"

    JEMALLOC_VERSION REGEX "${_version_regex}")

  string(REGEX REPLACE "${_version_regex}" "\\1"

    JEMALLOC_VERSION "${JEMALLOC_VERSION}")

  unset(_version_regex)

endif()



find_package_handle_standard_args(Jemalloc DEFAULT_MSG

  JEMALLOC_LIBRARY JEMALLOC_INCLUDE_DIR)

include(FindPackageHandleStandardArgs)

# handle the QUIETLY and REQUIRED arguments and set JEMALLOC_FOUND to TRUE

# if all listed variables are TRUE and the requested version matches.

find_package_handle_standard_args(Jemalloc REQUIRED_VARS

                                  JEMALLOC_LIBRARY JEMALLOC_INCLUDE_DIR

                                  VERSION_VAR JEMALLOC_VERSION)



get_property(_type CACHE JEMALLOC_ROOT PROPERTY TYPE)

if(_type)

  set_property(CACHE JEMALLOC_ROOT PROPERTY ADVANCED 1)

  if("x${_type}" STREQUAL "xUNINITIALIZED")

    set_property(CACHE JEMALLOC_ROOT PROPERTY TYPE PATH)

  endif()

endif()



mark_as_advanced(JEMALLOC_ROOT JEMALLOC_LIBRARY JEMALLOC_INCLUDE_DIR)

if(JEMALLOC_FOUND)

  set(JEMALLOC_LIBRARIES    ${JEMALLOC_LIBRARY})

  set(JEMALLOC_INCLUDE_DIRS ${JEMALLOC_INCLUDE_DIR})

endif()



mark_as_advanced(JEMALLOC_INCLUDE_DIR JEMALLOC_LIBRARY)

include/BooPHF.hpp

+395 −52

File changed.

Preview size limit exceeded, changes collapsed.

include/FastxParser.hpp

+14 −1
Original line number Diff line number Diff line
@@ -21,7 +21,7 @@ extern "C" { 


#if __cplusplus >= 201402L

#include <memory>

using std::make_unique

using std::make_unique;

#else



#include <cstddef>
@@ -121,8 +121,10 @@ public: 
  FastxParser(std::vector<std::string> files, std::vector<std::string> files2,

              uint32_t numConsumers, uint32_t numParsers = 1,

              uint32_t chunkSize = 1000);



  ~FastxParser();

  bool start();

  bool stop();

  ReadGroup<T> getReadGroup();

  bool refill(ReadGroup<T>& rg);

  void finishedWithGroup(ReadGroup<T>& s);
@@ -135,7 +137,17 @@ private: 
  std::vector<std::string> inputStreams2_;

  uint32_t numParsers_;

  std::atomic<uint32_t> numParsing_;



  // NOTE: Would like to use std::future<int> here instead, but that

  // solution doesn't seem to work.  It's unclear exactly why

  // see (https://twitter.com/nomad421/status/917748383321817088)

  std::vector<std::unique_ptr<std::thread>> parsingThreads_;



  // holds the results of the parsing threads, which is simply equal to

  // the return value of kseq_read() for the last call to that function.

  // A value < -1 signifies some sort of error.

  std::vector<int> threadResults_;



  size_t blockSize_;

  moodycamel::ConcurrentQueue<std::unique_ptr<ReadChunk<T>>> readQueue_,

      seqContainerQueue_;
@@ -145,6 +157,7 @@ private: 


  std::vector<std::unique_ptr<moodycamel::ProducerToken>> produceReads_;

  std::vector<std::unique_ptr<moodycamel::ConsumerToken>> consumeContainers_;

  bool isActive_{false};

};

}

#endif // __FASTX_PARSER__