[Biojava-dev] Fwd: [Biojava-l] file i/o with ArrayList

[Peter Cock]

On Fri, Feb 13, 2015 at 9:53 AM, stefan harjes <stefanharjes at yahoo.de> wrote:
> Hi Erik,
>
> thanks for the offer, but the little mistake with the enumeration was very
> quick to find. There is an increment of one added to the start position of
> each location for some reason. If you change it from 1 to 0, the sequence
> location start positions are no longer incremented.
>
> you can find it in line 284 of GenericInsdcHeaderFormat.java
>
> Cheers
> Stefan

Erik said the code was copied and translated from Biopython,
in which case we deliberately adjust the start position on parsing
*and* writing to use Python style slice counting, rather than the
INSDC feature table one-based counting.

I would first check the BioJava policy on feature coordinates,
it may be the bug is actually in the BioJava GenBank parser?

Regards,

Peter