[maker-devel] Patch for a bug with repeat gff

[Anthony Bretaudeau]

Hello,
I have just tested with 2.28b: the problem is still there, and my fix 
works on this version too.
Cheers
Anthony

On 10/06/2013 18:13, Carson Holt wrote:
> Could you use MAKER version 2.28 instead (launch with maker -a if it still
> fails).
>
> Thanks,
> Carson
>
>
>
> On 13-06-10 11:48 AM, "Anthony Bretaudeau"
> <anthony.bretaudeau at rennes.inra.fr> wrote:
>
>> Hello,
>> I am running Maker 2.27b on an insect genome, and I use a gff file
>> containing some repeat positions (rm_gff option in maker_opts.ctl).
>>
>> I encountered an error on 10 scaffolds (the genome contains ~40000
>> scaffolds) : "substr outside of string" (similar to this post:
>> http://gmod.827538.n3.nabble.com/substr-outside-of-string-td4031889.html).
>>
>> After a lot a debugging, it turns out the problem came from the code of
>> "phathits_on_chunk" function in lib/GFFDB.pm, near line 539: there is a
>> SQL query that fetches features that overlap with the border of the
>> sequence chunk.
>> The problem is that it also fetches features that are completely outside
>> of the chunk in the same region. This produces an error when maker tries
>> to mask the sequence as it does a substr outside the string.
>>
>> I fixed it by patching lib/repeat_mask_seq.pm, near line 138:
>> I replaced:
>>            substr($$seq, $b -1 , $l, "$replace"x$l);
>> By:
>>        if ($b < length($$seq)) {
>>            substr($$seq, $b -1 , $l, "$replace"x$l);
>>        }
>>
>> I don't know if there is a more elegant solution, but this seems to
>> solve the problem.
>>
>> Cheers
>> Anthony
>>
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>