PSI -- Pan-genome Seed Index

This is an implementation of the method introduced in:

Ghaffaari, A. & Marschall, T. Fully-sensitive seed finding in sequence graphs using a hybrid index Bioinformatics, 2019, 35, i81-i89

How to Install

Dependencies

Minimum requirements

PSI uses many features introduced in C++17. In order to work with it, you need a C++17 compliant compiler first. It has been tested for these compilers:

Compiler	Version
GCC	8.3, 9.2, 10.2.0

PSI is a header-only library. However, it depends on a few external libraries to work:

• CMake >=3.10
• Zlib
• BZip2

Bundled dependencies

There are a few more dependencies that is bundled with PSI; i.e. PSI can install them for you. If you want PSI to to do so, specify -DUSE_BUNDLED_ALL=on when running cmake (explained later). These dependencies are:

• SeqAn, version 2.4.0
• GUM, version 0.1.1
• kseq++, version 0.2.3
• PairG, version 0.2.0

PSI build script will skip those dependencies that are already installed on your system. Besides, installing each dependency can be individually enabled or disabled by setting -DUSE_BUNDLED_<library> to on or off respectively.

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NOTE If the bundled version of SeqAn did not work for any reason, install it manually. Make sure that seqan-2.pc configuration file has been installed too. On Debian-based operating systems, the easiest way to install SeqAn might be using the package manager:

$ sudo apt install libseqan2-dev

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Installation

To install PSI (recommended):

$ git clone https://github.com/cartoonist/psi.git
$ mkdir psi/build
$ cd psi/build
$ cmake -DCMAKE_BUILD_TYPE=Release -DKokkos_ENABLE_OPENMP=TRUE -DUSE_BUNDLED_ALL=on ..
$ make
$ sudo make install

Use PSI

There are two ways to include PSI into your project:

As a git submodule

If you are using CMake, the library can be added to your project as a git submodule. Then, calling add_subdirectory(path/to/psi) in the corresponding CMakeLists.txt file exports psi::psi target. The exported target defines include directories, transitive dependencies, and compiler flags required for building the project.

TODO: As an external dependency

Install the PSI as an external dependency. If you are using CMake find_package will import psi::psi target to which can be used to link your project.

If you are not using CMake, the same information can also be retrieved using pkg-config. Or just take a look at <INSTALL_PREFIX>/lib/pkgconfig/psi.pc.

Development

In order to build the tests or auxiliary tools, just turn on BUILD_TESTING or BUILD_PSI_AUX_TOOLS options when running cmake:

$ cmake -DCMAKE_BUILD_TYPE=Debug -DKokkos_ENABLE_OPENMP=TRUE -DBUILD_TESTING=on -DBUILD_PSI_AUX_TOOLS=on ..