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Pjotr Prins a79ae9713d Added license info for included undeaD code 4 years ago
bio Merge branch 'sambamba' of into sambamba 4 years ago
contrib/undead Added undead.cstream: sambamba strip_bcf_header.d still uses it 4 years ago
examples fixed with proper undead import path 4 years ago
test fix the module imports for test 4 years ago
.gitignore backup the old directory and module structure 4 years ago
.travis.yml test osx build 6 years ago
LICENSE changed license to MIT 9 years ago
Makefile fix undead import dir 4 years ago Added license info for included undeaD code 4 years ago Release 0.2.1 4 years ago
VERSION Release 0.2.1 4 years ago
dub.json fixed typo 4 years ago

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.


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

It is possible to create a recent build container with GNU guix

guix environment -C guix --ad-hoc ldc dub zlib gdb --network


With gdb, switch off the handlers

handle SIGUSR1 SIGUSR2 nostop noprint

It can be passed in from the command line

gdb -iex "handle SIGUSR1 SIGUSR2 no stop noprint" biod_test


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.