[Biojava-dev] GFF3 Parser upgrade

[Carmelo Foti]

Hi,
I've been using biojava for a while, and I'm very grateful to all the
developer.
I was not satisfied with the GFF access lib performance, so i decided to
add a feature.
Each time a gff is read, a List of attributes can be specified. If any of
the features has one of the attributes, it will be indexed for fast access.
If it doesn't, normal behavior is applied, so it's 100% compatible with old
code.
This is extremely useful for large gff. For example, in a simple program
that access the Ensembl transcriptoma, times drop from 277m34s  to  0m57s
using a 8 core machine. (please note that in both cases ~54s of the total
time are used to initialize the program).
I'd like to merge my code to the project, is there any standard way to
submit a pull request through github?
Thank you.

Carmelo Foti,
Research assistant at Politecnico di Torino