You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
 
 
 
George Githinji d7b79b1fbc fixed with proper undead import path 3 years ago
bio fixed errors in undead import paths 3 years ago
contrib/undead qualifiedthe undead module names with proper namespace 3 years ago
examples fixed with proper undead import path 3 years ago
test fix the module imports for test 3 years ago
.gitignore backup the old directory and module structure 3 years ago
.travis.yml test osx build 5 years ago
LICENSE changed license to MIT 9 years ago
Makefile fix undead import dir 3 years ago
README.md Fixing dub build 3 years ago
RELEASE-NOTES.md Release 0.2.1 3 years ago
VERSION Release 0.2.1 3 years ago
dub.json fixed typo 3 years ago

README.md

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 makes use of D programming language features that make it possible to develop high performance bioinformatics tools (e.g. sambamba). D 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 several modules to 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.

Install

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

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

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

and run meson and ninja (see the meson branch of BioD)

dub meson ./build ninja -C ./build

to create a debug version

meson build --buildtype debug --reconfigure

Note that in the current version dub is not required for dependencies.

Debugging

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

Usage

See the examples directory for examples and usage.

Mailing list

The BioD mailing list

Contributing

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

License

BioD is licensed under the liberal MIT (expat) license.