[ensembl-dev] trouble with ldFeatureContainerAdaptor->fetch_by_VariationFeature

[Anja Thormann]

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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