https://github.com/edawson/tinygfa
A header-only GFA file indexer (think .fai for GFA files)
https://github.com/edawson/tinygfa
Last synced: 4 months ago
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A header-only GFA file indexer (think .fai for GFA files)
- Host: GitHub
- URL: https://github.com/edawson/tinygfa
- Owner: edawson
- License: mit
- Created: 2018-12-10T01:10:53.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-04-17T03:43:11.000Z (about 5 years ago)
- Last Synced: 2025-01-07T20:46:38.282Z (5 months ago)
- Language: C++
- Size: 75.2 KB
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
tinyGFA
-----------------
Parse, index and get random access to GFA files.
### Current Limitations
Right now, we only index the Sequence lines of the
GFA file. There is code to index other types of lines
but the implementation isn't yet finished.
### Overview
GFA files provide a way to represent graph data structures from
assemblies and variation graphs. GFA is analagous to FASTA for
graphs. We often want random access to FASTA sequences on disk
using the .FAI index format. tinyGFA seeks to bring the same
indexing utilities to GFA.
### Build / install
To use tinyGFA, add the below lines to your C++ code:
```
#include "tinyGFA/tinygfaidx.hpp"
#include "tinyGFA/pliib.hpp"
using namespace GFAIDX;
```
tinyGFA should build with gcc (or clang if you've got OpenMP).
To build, link the `.hpp` file and then build your code.
### Index format
The index format (gfai file) is similar to the fasta index (fai) format,
but it includes an extra field to indicate what line type is indexed.
### Future Developments
1. Index rGFA paths, generating one index per static path
2. Streaming IO of GFA lines (using callback functions)
3. CUDA-supported data structures (but without hurting host functionality!)