[gt-users] gff3 parser

[Gordon Gremme]

> ok. i think i've resolved this:
> http://gist.github.com/62770
>
> for a.gff of:
> ##gff-version 3
> 1   ucb gene    2   2   .   -   .   ID=geneA
> 1   ucb gene    2   2   .   +   .   ID=geneB
>
> and b.gff of:
> gff-version 3
> 1   ucb gene    4   4   .   -   .   ID=geneA
>
> it gives:
>
> $ bin/gt gff3 -retainids a.gff b.gff 2>/dev/null
> ##gff-version   3
> ##sequence-region   1 2 2
> 1       ucb     gene    2       2       .       -       .       ID=geneA
> ###
> 1       ucb     gene    2       2       .       +       .       ID=geneB
> ###
> ##sequence-region   1 4 4
> 1       ucb     gene    4       4       .       -       .       ID=geneA.1
> ###
>
>
>
> and if i add another c.gff that's same as b.gff, it creates geneA.2

Ok, great! Could you add a test to testsuite/gt_gff3_include.rb to
test the new behaviour and make sure your code doesn't break the old
behaviour? It currently breaks some tests, just call testsuite.rb
-keywords gt_gff3 to check for yourself.

Gordon