Nelze vybrat více než 25 témat Téma musí začínat písmenem nebo číslem, může obsahovat pomlčky („-“) a může být dlouhé až 35 znaků.
Pjotr Prins 9844240ba4 Fix merge před 1 rokem
bio A bunch of changes to fix před 1 rokem
contrib/undead Fix undead unti test před 1 rokem
examples fixed with proper undead import path před 2 roky
test A bunch of changes to fix před 1 rokem
.gitignore backup the old directory and module structure před 2 roky
.travis.yml test osx build před 4 roky
LICENSE changed license to MIT před 7 roky
Makefile Fix merge před 1 rokem Fix merge před 1 rokem Version bump and release notes před 1 rokem
VERSION Version bump and release notes před 1 rokem
dub.json Fix merge před 1 rokem

BioD Build Status DUB Package

BioD is a fast and memory efficient bioinformatics library written in the D programming language whose aim is to:

  • Provide a platform for developing high-performance computational biology applications using the D programming language through
    • Automatic parallelization of tasks where possible
    • Avoiding unnecessary memory allocations

Why BioD?

BioD leverages on D programming language features to develop high performance bioinformatics tools (e.g. sambamba). The D programming language is both a low and high-level hybrid object orientated and functional (OOP/FP) programming language with templating/generic features are far easier than that of C++.

D programming language resources

Current development

Our aim is to provide a set of D modules to manipulate and work with biological datasets. BioD provides modules for manipulating high throughput data formats by provifing fast and easy to use native BAM file reader and writer with ability to iterate a BAM file a read at a time,a nucleotide at a time (pileup) or via a sliding window.

Note the current Bamreader bails out on recent versions of the LDC compiler. See also


The current default is to provide the path to the checked out repo to the D-compiler. For example,

DFLAGS = -wi -I. -IBioD -g

Build environment

After installing ldc and dub

dub test

On a recent Debian (>201911) you can install ldc and compile BioD with

make check

It is possible to create a recent build container with the GNU guix transactional package manager

guix environment -C guix --ad-hoc ldc dub zlib gdb binutils-gold vim --network

after getting dropped in the container simply run dub.

If you want to use the make file instead (not requiring the network) use

guix environment -C guix --ad-hoc ldc zlib gdb make binutils-gold vim --no-grafts
make -j 4
make check


When using gdb, switch off these handlers

handle SIGUSR1 SIGUSR2 nostop noprint

It can be passed in from the command line

gdb -ex 'handle SIGUSR1 SIGUSR2 nostop noprint' --args ./biod-test-library


See the examples directory for examples and usage.

Mailing list

The BioD mailing list


Simply clone the repository on github and put in a pull request.

BioD contributors and support

See contributors. For support use the issue tracker or contact


BioD is free software and licensed under the MIT (expat) license.

BioD includes some files from the undeaD project in ./contrib which are published under a Boost license. This code should be phased out in time.