[ensembl-dev] Uninitialized variable in reverse in Sequence.pm
Andrew Barron
ab5 at sanger.ac.uk
Thu Sep 4 19:49:02 BST 2014
Sent from my iPhone
> On 4 Sep 2014, at 17:19, "Sarah Hunt" <seh at ebi.ac.uk> wrote:
>
>
> Hi James,
>
> What naming convention is used in genome.fa? This problem has been reported previously with sequences named 'chr1' etc. rather than the Ensembl standard '1' etc. This causes a problem for the hgvs trancsript level annotation.
>
> Best wishes,
>
> Sarah
>
>> On 03/09/2014 21:02, James Knight wrote:
>> I am running VEP, from release 76, using —offline, --everything and "--fasta genome.fa" (to get HGVS annotations while still offline). When I do this, this error message is output numerous times:
>>
>> Use of uninitialized value in reverse at /home/jk2269/soft/ensembl-tools-release-76/scripts/variant_effect_predictor/Bio/EnsEMBL/Utils/Sequence.pm line 90.
>>
>> Is this a bug?
>>
>>
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