Fix transcript mismatch warning message

[dglemos]

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]

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

[likhitha-surapaneni]

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 Ensembl/ensembl-io#172 is merged!