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

[Wallace Ko]

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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