[ensembl-dev] trouble with ldFeatureContainerAdaptor->fetch_by_VariationFeature

[andrew126 at mac.com]

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