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# BioD [![Build Status](https://travis-ci.org/biod/BioD.svg?branch=master)](https://travis-ci.org/biod/BioD) [![DUB Package](https://img.shields.io/badge/dub-v0.1.0-red.svg)](https://code.dlang.org/packages/biod)
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[BioD](https://github.com/biod/BioD) is a fast and memory efficient bioinformatics library written in the [D programming language](http://www.dlang.org)
whose aim is to:
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* Provide a platform for developing high-performance computational biology applications using the [D programming language](http://www.dlang.org) through
- Automatic parallelization of tasks where possible
- Avoiding unnecessary memory allocations
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## Why BioD?
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BioD leverages on [D programming language](http://www.dlang.org)
features to develop high performance bioinformatics tools
(e.g. [sambamba](https://github.com/biod/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++.
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## D programming language resources
* [Programming in D](http://ddili.org/ders/d.en/index.html) is online by Ali Çehreli.
* [The D Programming Language](https://www.amazon.com/D-Programming-Language-Andrei-Alexandrescu/dp/0321635361) by Andrei Alexandrecu (great book, slightly out of date)
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* [The D Cookbook](https://www.amazon.com/D-Cookbook-Adam-D-Ruppe/dp/1783287217) by Adam D. Ruppe
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## 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.
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## Install
The current default is to provide the path to the checked out repo to
the D-compiler. For example,
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DFLAGS = -wi -I. -IBioD -g
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## Build environment
After installing ldc and dub
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dub
dub test
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It is possible to create a recent build container with the
[GNU guix](https://www.gnu.org/software/guix/) transactional package
manager
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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
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## Debugging
When using gdb, switch off these handlers
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handle SIGUSR1 SIGUSR2 nostop noprint
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It can be passed in from the command line
gdb -ex 'handle SIGUSR1 SIGUSR2 nostop noprint' --args ./biod-test-library
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## Usage
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See the [examples directory](examples)
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for examples and usage.
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## Mailing list
[The BioD mailing list](https://groups.google.com/forum/#!forum/dlang_biod)
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## Contributing
Simply clone the repository on github and put in a pull request.
## BioD contributors and support
See
[contributors](https://github.com/biod/BioD/graphs/contributors). For
support use the [issue tracker](https://github.com/biod/BioD/issues) or contact
* [Pjotr Prins](https://github.com/pjotrp)
* [George Githinji](https://github.com/George-Githinji)
* [Prasun Anand](https://github.com/prasunanand)
## License
BioD is free software and licensed under the MIT (expat) [license](./LICENSE).
BioD includes some files from the
[undeaD project](https://github.com/dlang/undeaD) in ./contrib which
are published under a Boost license. This code should be phased out in time.