BioD

Introduction

BioD is an open source software library for analysis of biological sequence and high-throughput data generated in genomics and life-sciences written using the D programming language. BioD provides a platform for developing fast and efficient bioinformatics applications used for processing high-throughput biological data and manipulating common bioinformatics file formats. BioD tries to avoid heap allocations and tasks are parallelized to take advantage of available CPUs. The current code base provides efficient native processing of BAM files, a convinient alphabet and an abstraction for representing biological sequence data.

Why D?

D is a compiled multi-paradigm systems programming language that emphasizes memory safety, correctness and offers the same speed and effieciency as C/C++ and a reputation for fast code compilation. The LDC or GDC compilers provide some of the most efficient and fast binaries, in addition, the LDC compiler provides implicit cross-compilation. Futhermore GDC will be included as part of the GCC compiler.

Unit tests

Every non-trivial algorithm in the library is covered by unittests, which can be easily run from the command line (see below). Whenever you find out that something doesn't work correctly, please report an issue, and the test suite will grow once it's fixed!

Compiling

A recent D compiler is required to work with BioD. BioD is supported on Linux and Macos platforms. It has not been tested on the Windows platform.

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$ git clone https://github.com/biod/BioD.git
$ cd BioD/test
$ rdmd -I.. -unittest unittests.d

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$ cd ../examples
$ rdmd -I.. example1.d
$ dmd -I.. -i example1.d // compile an example
$ ./example1 //run the compiled binary

License

BioD is provided under the MIT (expat) license.