[gt-users] gff3 parser

[Sascha Steinbiss]

Brent Pedersen wrote:
>> The GT_MEM_BOOKKEEPING mechanism is greate to detect memleaks, but
>> fixing is easier with valgrind --tool=memcheck.
>> It gives you the complete ``stack''. See http://valgrind.org/, if you
>> don't know it already.
> bah. i was trying to avoid becoming a c programmer.

It's not so bad, you know ;)

>>> should i just change the tests or do you want to keep the original behavior when
>>> the retainids is not used?
>> Please keep the original behaviour.
> ok. all tests pass with this patch:
> http://gist.github.com/62770/

Thanks, that seems to do the trick. Nice work!

We should maybe generally discuss whether ID renaming may be 
counterproductive in the case of multi-line features, e.g.

$ bin/gt gff3 -retainids testdata/multi_feature_simple.gff3
##gff-version   3
##sequence-region   ctg123 1 1497228
warning: feature ID "CDS1" not unique: changing to CDS1.1
ctg123	.	gene	1000	9000	.	+	.	ID=gene1
ctg123	.	CDS	1201	1500	.	+	0	ID=CDS1;Parent=gene1
ctg123	.	CDS	3000	3902	.	+	0	ID=CDS1.1;Parent=gene1

breaks the "same-ID" rule for the multi-line features. I am not sure 
whether this may lead to problems or not...
Any comments?

Sascha

-- 
Sascha Steinbiss
Center for Bioinformatics
University of Hamburg
Bundesstr. 43
20146 Hamburg
Germany

Email:  steinbiss at zbh.uni-hamburg.de
URL:    http://www.zbh.uni-hamburg.de/steinbiss
Phone:  +49 (40) 42838 7322
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