[Bioperl-pipeline] Annotation+Transformers

[Juguang Xiao]

>>
>> I also had such problem, Shawn, do you remember that I added 
>> get_all_Contig_name in RawContigAdaptor in  my local code, and never 
>> submit into ensembl because i am not sure if they like this 
>> no-harm-but-not-necessary-for-them sub.  I prefer to have  2 own 
>> module, rather than changing the ensembl code.
>>
>
> You mean creating another supplementary module?
> Isn't neater to just add the subroutine to ensembl?
> Its something that ensembl used to have anyway....

That is also policy question I am keen to get answered, that if it is 
acceptable by ensembl guys to have extra committed methods which is 
other project specific, so far.

Personally, I also do not like the way to create such 2 modules, I 
prefer to add get_all_Contig_name in 
Bio::EnsEMBL::DBSQL::RawContigAdaptor.

Juguang