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

[Wallace Ko]

Thanks Will! The patch works great.

Regards,
Wallace Ko
L3 Bioinformatics

On Mon, Jun 26, 2017 at 4:32 PM, William McLaren <wm2 at ebi.ac.uk> wrote:

> 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:
>
>    1. The methods results_from_cache and results_from_seq return an array
>    of hash
>    <https://github.com/Ensembl/VEP_plugins/blob/b25f865c97a30ffdca18f63040f715032578ea8a/GeneSplicer.pm#L186-L187>
>    .
>    2. The method compare_results returns the array (lost and diff) that
>    contains same hashes
>    <https://github.com/Ensembl/VEP_plugins/blob/b25f865c97a30ffdca18f63040f715032578ea8a/GeneSplicer.pm#L190-L191> (for
>    case of diff, it modifies
>    <https://github.com/Ensembl/VEP_plugins/blob/b25f865c97a30ffdca18f63040f715032578ea8a/GeneSplicer.pm#L332-L334>
>    score and confidence of hash in first array).
>    3. When formatting result
>    <https://github.com/Ensembl/VEP_plugins/blob/b25f865c97a30ffdca18f63040f715032578ea8a/GeneSplicer.pm#L220>,
>    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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