|George Githinji d7b79b1fbc||2 years ago|
|bio||2 years ago|
|contrib/undead||2 years ago|
|examples||2 years ago|
|test||2 years ago|
|.gitignore||2 years ago|
|.travis.yml||4 years ago|
|LICENSE||7 years ago|
|Makefile||2 years ago|
|README.md||2 years ago|
|RELEASE-NOTES.md||2 years ago|
|VERSION||2 years ago|
|dub.json||2 years ago|
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++.
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.
The current default is to provide the path to the checked out repo to the D-compiler. For example,
DFLAGS = -wi -I. -IBioD -g
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.
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.
Simply clone the repository on github and put in a pull request.
BioD is licensed under the liberal MIT (expat) license.