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README: reformat, updated instructions

sambamba
Pjotr Prins 3 years ago
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      README.md

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README.md

@ -9,51 +9,51 @@ whose aim is to:
## Why BioD?
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++.
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++.
## D programming language resources
* [The D Programming Language](https://www.amazon.com/D-Programming-Language-Andrei-Alexandrescu/dp/0321635361) by Andrei Alexandrecu
* [Programming in D](http://ddili.org/ders/d.en/index.html) by Ali Çehreli.
* [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by Andrei Alexandrecu (great book, slightly out of date)
* [The D Cookbook](https://www.amazon.com/D-Cookbook-Adam-D-Ruppe/dp/1783287217) 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.
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.
## Install
The current default is to provide the path to the checked out repo to the D-compiler. For example,
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`
After installing ldc and dub
and run meson and ninja (see the meson branch of BioD)
dub
dub test
`dub
meson ./build
ninja -C ./build`
to create a debug version
`meson build --buildtype debug --reconfigure`
It is possible to create a recent build container with GNU guix
Note that in the current version dub is not required for dependencies.
`guix environment -C guix --ad-hoc ldc dub zlib gdb --network`
## Debugging
With gdb, switch off the handlers
` handle SIGUSR1 SIGUSR2 nostop noprint`
`handle SIGUSR1 SIGUSR2 nostop noprint`
It can be passed in from the command line

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