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biod ~bio2

Bioinformatics library in D (utils for working with SAM, BAM, SFF formats)


To use this package, run the following command in your project's root directory:

Manual usage
Put the following dependency into your project's dependences section:

InfoReference

BioD Build Status DUB Package

BioD is a fast and memory efficient bioinformatics library written in the D programming language.

BioD aims to:

  • Provide a platform for writing high-performance bioinformatics applications in D. BioD achieves this by:
  • automatic parallelization of tasks where possible for example reading and writing BAM files
  • reducing the GC overhead by avoiding unnecessary memory allocations
  • Offer support for manipulating common biological data formats

Install

The current default is to provide the path to the checked out repo to the D-compiler. For example in sambamba we use 

DFLAGS = -wi -I. -IBioD -g

Usage

See the examples directory for examples and usage.

BioD is also a crucial part of the sambamba tool.

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.

Authors:
  • Artem Tarasov
  • Pjotr Prins
Dependencies:
undead
Versions:
0.2.3 2019-Jun-01
0.2.2 2019-Mar-16
0.2.1 2018-Oct-04
0.2.0 2018-Sep-15
0.1.0 2016-Jun-14
Show all 11 versions
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Short URL:
biod.dub.pm