[ensembl-dev] Uninitialized variable in reverse in Sequence.pm

[Sarah Hunt]

Hi Jim,

Good to hear that sorted it. Thanks for letting us know.

Sarah

On 04/09/2014 18:48, James Knight wrote:
> Switching to the Ensembl standard reference accessions does avoid this issue, and I no longer get the error with those accessions.
>
> Jim
>
> On Sep 4, 2014, at 12:19 PM, 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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