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Hi Oliver,<br>
<br>
Thanks for the detailed report. This was a similar issue with a stop
inserted before the stop not being handled well. It is fixed in
branch78 so the consequence of the variant has changed from
'stop_gained' to 'stop_retained'. The HGVS string reflects the
synonymous status.<br>
<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
<br>
<div class="moz-cite-prefix">On 03/02/2015 16:52, Homann, Oliver
wrote:<br>
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<p class="MsoNormal"><span style="color:#1F497D">Apologies,
forgot to clarify that the error occurs in line 1221 of the
new version of TranscriptVariationAllele.pm:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> 1221
unless( $hgvs_notation->{ref} eq "-"){<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> 1222
$hgvs_notation->{ref} =
Bio::SeqUtils->seq3(Bio::PrimarySeq->new(-seq =>
$hgvs_notation->{ref}, -id => 'ref', -alphabet =>
'protein')) || "";<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> 1223 }<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Oliver<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">
<a class="moz-txt-link-abbreviated" href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [<a class="moz-txt-link-freetext" href="mailto:dev-bounces@ensembl.org">mailto:dev-bounces@ensembl.org</a>]
<b>On Behalf Of </b>Homann, Oliver<br>
<b>Sent:</b> Tuesday, February 03, 2015 8:50 AM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] VEP (ver78)
TranscriptVariationAllele.pm unitialized value error
with --hgvs enabled<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Hello Sarah,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Your fix worked
for all but one of my ‘uninitialized value’ errors. Would
you mind trying to track down the issue with this remaining
problematic entry?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">#CHROM
POS ID REF ALT QUAL
FILTER INFO FORMAT SAMPLENAME<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">19
42355761 rs374945441 C
CTAGAAA 885.10 .
AC=1;AF=5.556e-03;AN=180;BaseQRankSum=-1.922e+00;DB;DP=2670;FS=2.561;GQ_MEAN=75.28;GQ_STDDEV=91.16;InbreedingCoeff=-0.0056;MLEAC=1;MLEAF=5.556e-03;MQ=60.00;MQ0=0;MQRankSum=-2.160e-01;NCC=0;QD=9.83;ReadPosRankSum=0.353;SOR=0.669
GT:AD:DP:GQ:PL 0/0:17,0:17:34:0,34,505<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Oliver<o:p></o:p></span></p>
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