https://github.com/ggonnella/bfa

BFA, draft proposal of a binary GFA-like format
https://github.com/ggonnella/bfa

Last synced: 6 days ago
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BFA, draft proposal of a binary GFA-like format

• Host: GitHub
• URL: https://github.com/ggonnella/bfa
• Owner: ggonnella
• Created: 2016-09-20T17:26:13.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2016-09-20T17:40:57.000Z (over 8 years ago)
• Last Synced: 2024-12-16T23:34:51.747Z (about 1 month ago)
• Language: Ruby
• Size: 398 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
The Graphical Fragment Assembly (GFA)

described under https://github.com/pmelsted/GFA-spec/blob/master/GFA-spec.md

is a proposed format which allows

to describe the product of sequence assembly and is implemented in the

RGFA class defined in the rgfa gem. This gem represents an extension of the

RGFA class, which implements a binary format, BFA, equivalent to RGFA.

## Installation

Please install RGFA prior to this.

https://github.com/ggonnella/RGFA

## Specification

The BFA format is described here:

https://github.com/ggonnella/bfa/tree/master/specification/bfa.pdf

## Poster

A conference poster describing RGFA and BFA has been presented at the

Genome Informatics 2016 conference.

The poster can be downloaded here:

https://github.com/ggonnella/bfa/tree/master/poster/poster.pdf

## Usage

require "rgfa" from the RGFA library and "bfa" from this library.

### GFA to BFA

To encode a GFA file into BFA, load it using g = RGFA.from_file(gfa_filename),

then write it to a BFA file using BFA::Writer.encode(bfa_filename, g).

### BFA to GFA

To decode a BFA file, use b = BFA::Reader.parse(bfa_filename). This will

create a RGFA object, which you can write to GFA using b.to_file(gfa_filename).