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tinyGFA

Parse, index and get random access to GFA files.

C/C++ CI for tinyGFA

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!)