[ensembl-dev] trouble with ldFeatureContainerAdaptor->fetch_by_VariationFeature

[andrew126 at mac.com]

Hi Anja,

Thanks for the quick fix.  After pull'ing my checkout of the 93 branch, I no longer see the error and I seem to get good LD results.  But it seems like the Tabix.pm query method no longer gets called in the same way?  That is, the debug code I put in that function doesn't seem to get called anymore, so I can't positively confirm what region has been sent to the function.  Was there some change, such that Tabix.pm->query no longer gets called?

Thanks.

Best,

Andrew

> On Sep 13, 2018, at 2:24 AM, Anja Thormann <anja at ebi.ac.uk> wrote:
> 
> 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 <mailto: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 <mailto: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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