[ensembl-dev] GeneSplicer not returning results due to updated cache

[William McLaren]

Hi Wallace,

Thanks for finding this and getting to the root of the problem. I’ve patched a fix to the plugin on the dev and release/89 branches.

https://github.com/Ensembl/VEP_plugins/commit/cb2bb3230320c704a0786604617c626f16a88423

Regards

Will McLaren
Ensembl Variation


On 26 June 2017 at 04:48:06, Wallace Ko (myko at l3-bioinfo.com) wrote:

Hi,

It is observed that the GeneSplicer plugin is only returning results for first result of the same variant.

It is caused by updated cache:
The methods results_from_cache and results_from_seq return an array of hash.
The method compare_results returns the array (lost and diff) that contains same hashes (for case of diff, it modifies score and confidence of hash in first array).
When formatting result, the map_ss_coords method modifies the end5 and end3 property of the cache. The cache now contains translated positions. Subsequent runs of the plugin on the same sequence grep overlapping results using the translated positions and thus no result is returned.
The quick fix I am using is to deep clone the values returned from results_from_cache and results_from_seq.

Regards,
Wallace Ko
L3 Bioinformatics
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