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

[Carson Holt]

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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