[ensembl-dev] trouble with ldFeatureContainerAdaptor->fetch_by_VariationFeature

[Anja Thormann]

Hi Andrew,

this has been fixed on release/93 branch. We pushed the code fix  <https://github.com/Ensembl/ensembl-variation/pull/226>to the release/93 branch. Please refresh your checkout and let us know if you encounter any problems with the code. Thank you for reporting the error.

Best wishes,
Anja

> On 11 Sep 2018, at 17:09, Anja Thormann <anja at ebi.ac.uk> wrote:
> 
> Hi Andrew,
> 
> thank you for the bug report. We are looking into what’s causing the error and will soon get back to you with a fix.
> 
> Thank you,
> Anja
> 
>> On 10 Sep 2018, at 09:08, andrew126 at mac.com wrote:
>> 
>> Hi,
>> 
>> This applies to Ensembl API v93.
>> 
>> I am occassionally getting failures from ldFeatureContainerAdaptor->fetch_by_VariationFeature with the following message:
>> 
>> 	You must specify a region in the format chr, chr:start or chr:start-end at /usr/local/ensembl/ak_API93/Bio-DB-HTS/lib/Bio/DB/HTS/Tabix.pm line 104.
>> 
>> One of the failure instances occured for variation feature rs12445289 (its chr 16 mapping), and I was able to see that this region was provided to Tabix.pm:
>> 
>> 	16:-81648-918353
>> 
>> rs12445289 is at location 418,353 on chr 16, and I was using a max_snp_distance of 500000, which seems to explain the start and end values sent to Tabix, but Tabix.pm does not seem prepared to handle a negative start position (I think it wants to see only a digit after the first colon).
>> 
>> fetch_by_VariationFeature for chr-16 rs12445289 +/- 500,000 does not fail throw any error for Ensembl API v90, fwiw
>> 
>> Is there a fix possible for this?
>> 
>> Thanks for any help.
>> 
>> Best,
>> 
>> Andrew
>> 
>> 
>> 
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