[EMBOSS] seqret segfault (refseq protein sequence, indexed with dbxflat)

[Jan T Kim]

Dear Peter,

this fixes the problem on my laptop so I'll roll this out on the
Ubuntu box as well.

Thank you for your quick reply, and apologies for forgetting the
attachment.

(I've been comparing the two records but I would not have guessed
that the difference in length of the coded_by value is the problem --
not without using the source anyway.)

Best regards, Jan

On Fri, Mar 01, 2013 at 07:03:44PM +0000, Peter Rice wrote:
> Dear Jan,
> ?
> > I've run into a weird problem with seqret after downloading the complete
> > protein refseq database and indexing that with dbxflat. The problem
> > seems to be triggered by a rare condition, so far I've only encountered
> > it with accession ZP_10312765:
> 
> The problem is in ajax/core/ajfeatwrite.c in function featTagSwissWrapC (so it will only affect Swissprot format feature output).
> ?
> Variable j is declared ajulong but should be ajlong (signed, so it can have a value of -1 in this case).
> ?
> If you change the line to
> ?
> ??? ajlong j;
> ?
> and rebuild, that should fix it.
> ?
> I will check the other wrapping functions in case they have a similar problem with other inputs.
> ?
> Again, many thanks for finding it.
> ?
> Peter Rice
> EMBOSS Team

-- 
 +- Jan T. Kim -------------------------------------------------------+
 |             email: jttkim at gmail.com                                |
 |             WWW:   http://www.jtkim.dreamhosters.com/              |
 *-----=<  hierarchical systems are for files, not for humans  >=-----*