<div dir="ltr">Hi Oliver,<div><br></div><div>Are you able to provide a sample input file that recreates this problem?</div><div><br></div><div>There is code in place in the VEP to restore the order as it was in the input file; if you have evidence that this isn't working then it would be useful to see it. The ordering code has been in place since release 75, so if you are using 74 or earlier then obviously this doesn't apply!</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 11 February 2015 at 23:38, Homann, Oliver <span dir="ltr"><<a href="mailto:ohomann@amgen.com" target="_blank">ohomann@amgen.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="color:#1f497d">Hello Sarah,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d">I’m writing to confirm that the issue was solved, and also to report another very minor issue. I presume VEP is intended to output data in the same order as the records of the VCF input. This is almost entirely
the case for my data, but I find that a set of MT records gets inserted into the middle of the ChrY records near the end of the output. I’ve resorted the files to address this inconsistency, but I wanted to bring it to your attention. If I had to venture
a wild guess, perhaps this is due an error with multi-threading logic, in which the final records to return are flushed out of order?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d">Regards,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d">Oliver<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d"><u></u> <u></u></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 href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>]
<b>On Behalf Of </b>Sarah Hunt<br>
<b>Sent:</b> Thursday, February 05, 2015 4:22 AM</span></p><div><div class="h5"><br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] VEP (ver78) TranscriptVariationAllele.pm unitialized value error with --hgvs enabled<u></u><u></u></div></div><p></p>
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</div><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
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>
<u></u><u></u></p>
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<p class="MsoNormal">On 03/02/2015 16:52, Homann, Oliver wrote:<u></u><u></u></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<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:</span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d"> 1221 unless( $hgvs_notation->{ref} eq "-"){</span><u></u><u></u></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')) || "";</span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d"> 1223 }</span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d">Regards,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d">Oliver</span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d"> </span><u></u><u></u></p>
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<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<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 href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [<a href="mailto:dev-bounces@ensembl.org" target="_blank">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</span><u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d">Hello Sarah,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d"> </span><u></u><u></u></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?</span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLENAME</span><u></u><u></u></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</span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d">Thanks,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d">Oliver</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""><br>
<br>
<br>
<u></u><u></u></span></p>
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</blockquote>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u> <u></u></span></p>
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