biod ~master

BioD

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

• Programming in D is online by Ali Çehreli.
• The D Programming Language by Andrei Alexandrecu (great book, slightly out of date)
• The D Cookbook by Adam D. Ruppe

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 https://github.com/biod/BioD/issues/53

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

After installing ldc and dub

dub
dub test

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

make
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

Debugging

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

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

• Pjotr Prins
• George Githinji
• Prasun Anand

License

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.