ToC
This page gives an example of how to use SeqAn in your application based on your own Makefiles. You should be able to adapt the descriptions to configure your build system and/or IDE.
Tip
SeqAn is a header-only library.
Simply adding its include folder to your include path or installing it globally makes it available to your program.
On GNU/Linux, BSD and macOS, always add -std=c++14 (or a newer standard) when building on the command line.
For XCode on macOS you need to set this option in the project settings.
As of Visual Studio 2015 our subset of C++14 is already available in all supported compilers.
On GNU/Linux, BSD and macOS, add -fopenmp unless you are using Clang versions older than 3.8.0.
For XCode on macOS OpenMP is not yet available.
With Visual Studio OpenMP is switched on by default.
Libraries
Add -lrt -lpthread to the compiler call.
Libraries
Add -lpthread -lexecinfo -lelf to the compiler call.
Misc
Also define -D_GLIBCXX_USE_C99=1 if you are using gcc-4.9.
It is recommended to compile your programs with as many warnings enabled as possible. This section explains which flags to set for different compilers.
The following flags are recommended:
-W -Wall -pedanticMaximal sensitivity of compiler against possible problems.
For Visual Studio, the following flags are recommended:
/W2 /wd4996 -D_CRT_SECURE_NO_WARNINGSExplanation:
/W2Warning level 2 is pretty verbose already. In the future, we will support level 3 without warnings in SeqAn code.
/wd4996Allows the use of some deprecated functions without warnings.
-D_CRT_SECURE_NO_WARNINGS ::Some C functions likesprintfare prone to incorrect usage and security holes. Replacing such calls does not have a high priority right now since SeqAn is usually not used on servers facing the outside world. Preprocessor Defines Affecting SeqAn ------------------------------------ There are certain preprocessor symbols that affect the behaviour of SeqAn. SEQAN_ENABLE_DEBUG ^^^^^^^^^^^^^^^^^^ possible value 0, 1 default 0 meaning If set to 1, assertions within SeqAn (SEQAN_ASSERT...) are enabled, they are disabled otherwise. Is forced to 1 ifSEQAN_ENABLE_TESTINGis true. This flag will internally always correspond to the inverse ofNDEBUG, i.e. setting it to 1 will forceNDEBUGto be undefined and setting it to 0 will forcefully setNDEBUG. SEQAN_ENABLE_TESTING ^^^^^^^^^^^^^^^^^^^^ possible value 0, 1 default 0 meaning This makes the code very slow, and should only be used when running the SeqAn unit tests. Has to be set to 1 for tests to work. SEQAN_ASYNC_IO ^^^^^^^^^^^^^^ possible value 0, 1 default 0 onFreeBSD/32BitandOpenBSD/*; 1 otherwise meaning Whether asynchronous input/output is available. SEQAN_HAS_EXECINFO ^^^^^^^^^^^^^^^^^^ possible value 0, 1 default depends on platform / existance of<execinfo.h>meaning This should almost always be set to 1 on non-Windows platforms! SEQAN_HAS_BZIP2 ^^^^^^^^^^^^^^^ possible value 0, 1 default 0 meaning If set to 1 then libbzip2 is expected to be available. You have to link against the library (e.g. add-lbz2to your linke rflags) andbzlib.hmust be in your include path. SEQAN_HAS_ZLIB ^^^^^^^^^^^^^^ possible value 0, 1 default 0 meaning If set to 1 then zlib is expected to be available. You have to link against the library (e.g. add-lzto your linker flags) andzlib.hmust be in your include path. Settings Projects Using Seqan ----------------------------- You normally want to have at least two build modes: one for debugging and one for optimized compiling. The following settings have to be applied to your IDE project/Makefiles (below is an example for a Makefile based project). Debug Builds ^^^^^^^^^^^^ Besides enabling debug symbols and disabling optimization, there are the following SeqAn specific settings to be applied. - Add SeqAn to your include path - DefineSEQAN_ENABLE_DEBUGto be1. This translates into the following GCC flags: :: -g -O0 -DSEQAN_ENABLE_DEBUG=1 -I${PATH_TO_SEQAN_INSTALL}/include Release/Optimized Builds ^^^^^^^^^^^^^^^^^^^^^^^^ Besides disabling debug symbols, enabling optimization and disabling assertions in the standard library, there are the following SeqAn specific settings to be applied. - Add SeqAn to your include path - DefineNDEBUG. This will make sure thatSEQAN_ENABLE_DEBUGis 0 and also other STL includes of your program are not slowed down. This translates into the following GCC flags: :: -O3 -DNDEBUG -I${PATH_TO_SEQAN_INSTALL}/include .. caution:: While some guides tell you to not use-O3this is absolutely crucial for SeqAn based applications to perform well. Unoptimized builds are slower by multiple factors! An Example Project Based On Makefiles ------------------------------------- We will create a project with good old Makefiles and GCC. The program will not do much but can serve as a minimal example on how to use SeqAn with your own build process. You should be able to adapt this guide to your favourite build system or IDE. The example project can be found inutil/makefile_project. The project layout looks like this: :: . |-- Makefile.rules |-- Makefile |-- README |-- debug | `-- Makefile |-- release | `-- Makefile `-- src `-- main.cpp main.cpp ^^^^^^^^ We have one directorysrcfor source files. The filemain.cpplooks as follows: .. includefrags:: util/makefile_project/src/main.cpp :language: cpp It includes SeqAn headers just as you would within the SeqAn CMake framework. Now, consider the contents of the Makefiles: Makefile.rules ^^^^^^^^^^^^^^ Contains the necessary commands to build the object file for the programmain.cppand then make an executeablemainfrom it and clean targets. This file is included from the filesrelease/Makefileanddebug/Makefile. .. includefrags:: util/makefile_project/Makefile.rules :language: make Makefile ^^^^^^^^ Allows to build both debug and release builds by callingmake debug,make releaseormake allfrom the project directory. Removes all binaries withmake clean. .. includefrags:: util/makefile_project/Makefile :language: make debug/Makefile, release/Makefile ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The filedebug/Makefilelooks as follows. .. includefrags:: util/makefile_project/debug/Makefile :language: make The filerelease/Makefilelooks as follows. .. includefrags:: util/makefile_project/release/Makefile :language: make These Makefiles include the fileMakefile.rules. They add build type specific arguments to the variables$(CXXFLAGS). For debug builds, debug symbols are enabled, optimization level 0 is chosen, testing is enabled in SeqAn and debugging is disabled. For release builds, debug symbols are not, optimization level 3 is chosen, testing and debugging are both disabled in SeqAn. For good measure, we also disable assertions in the C library with-DNDEBUG. Notes ^^^^^ Above we added the include path to SeqAn's include directory manually. By changing the include path, we can install the SeqAn library anywhere. For example, we could create a directoryincludeparallel tosrc, copy the release version of SeqAn into it and then change the include path of the compiler to point to this directory (value../include). Short Version ------------- +---------+---------------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | OS | Compiler | Flags | +=========+=====================+=============================================================================================================================================+ | Linux | GCC/Clang≥3.8/ICC |-I /path/to/seqan/include -std=c++14 -O3 -DNDEBUG -W -Wall -pedantic -fopenmp -lpthread -lrt| +---------+---------------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | BSD | GCC/Clang≥3.8/ICC |-I /path/to/seqan/include -std=c++14 -O3 -DNDEBUG -W -Wall -pedantic -fopenmp -lpthread -lexecinfo -lelf -D_GLIBCXX_USE_C99=1| +---------+---------------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | macOS | system's Clang |-I /path/to/seqan/include -std=c++14 -O3 -DNDEBUG -W -Wall -pedantic| +---------+---------------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | Windows | Visual Studio MSVC |/W2 /wd4996 -D_CRT_SECURE_NO_WARNINGS| +---------+---------------------+---------------------------------------------------------------------------------------------------------------------------------------------+ Adapt the include path to the actual place of SeqAn'sinclude`` folder!