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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
Apache License 2.0
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Fix transcript mismatch warning message #1788

Closed dglemos closed 1 week ago

dglemos commented 2 weeks ago

This update should be included in release/113.

The following warning message: Transcript-assembly mismatch in ".$hash->{Uploaded_variation} should not be printed when the option --use_given_ref is on.

The warning indicates there is a mismatch between RefSeq and Ensembl transcripts for the variant stored in $hash->{Uploaded_variation}.

dglemos commented 2 weeks ago

Failing:

not ok 30 - annotate_InputBuffer - SV reverts to overlap
#   Failed test 'annotate_InputBuffer - SV reverts to overlap'
#   at t/AnnotationSource_File_VCF.t line 444.
#     Structures begin differing at:
#          $got = undef
#     $expected = HASH(0x59e2380)

This error is not related to this update. Errors are probably a consequence of this PR: https://github.com/Ensembl/ensembl-vep/pull/1773

likhitha-surapaneni commented 2 weeks ago

Failing:

not ok 30 - annotate_InputBuffer - SV reverts to overlap
#   Failed test 'annotate_InputBuffer - SV reverts to overlap'
#   at t/AnnotationSource_File_VCF.t line 444.
#     Structures begin differing at:
#          $got = undef
#     $expected = HASH(0x59e2380)

This error is not related to this update. Errors are probably a consequence of this PR: #1773

Hi @dglemos, this may be fixed when https://github.com/Ensembl/ensembl-io/pull/172 is merged!

likhitha-surapaneni commented 4 days ago

Cherry-picked to release/113