<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">With Ensembl version 67, cvs download 2012-05-22 and VEP v 2.5, I’m getting a lot of errors in TranscriptVariationAllele.pm<div><br></div><div>This is an example of an offending input VCF record:</div><div>5 96232565 incomplete_terminal_codon_variant A ACC . . . GT:AB:AD:DP:GQ:PL 0/1:0.88:36,5:41:77.58:78,0,611 1/1:.:0,5:5:12.01:111,12,0</div><div><br></div><div>This record has 5 transcripts</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>ENST00000513084.1:c.1501_1502insCC</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>ENST00000379904.4:c.1366_1367insCC</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>ENST00000508077.1:c.488_489insCC</div><div><span class="Apple-tab-span" style="white-space:pre"> ENST00000510373.1:c.1501_1502insCC</span></div><div><span class="Apple-tab-span" style="white-space:pre"> ENST00000437043.3:c.1501_1502insCC</span></div><div><br></div><div>All five transcripts cause this error:</div><div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Use of uninitialized value in numeric lt (<) at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 980, <GEN9> line 3.</div></div><div><br></div><div><div>It looks like the error is actually caused by line 986</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>elsif( length($self->codon()) < 3 && $hgvs_notation->{type} ne "fs”){</div><div>because $self->codon() returns undef when $allele_len=2 and $vf_nt_len=0</div><div><br></div></div><div>Transcript ENST00000508077.1:c.488_489insCC causes two additional errors:</div><div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Use of uninitialized value in substitution (s///) at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 997, <GEN9> line 3.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 761, <GEN9> line 3.</div></div><div><br></div><div>For this transcript, $hgvs_notation->{ref} = '' and $hgvs_notation->{alt} = undef, which seems to cause these errors.</div><div><br></div><div><br></div><div><br></div><div><div apple-content-edited="true"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-family: Helvetica; font-size: 12px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: 10px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><p class="MsoNormal"><font class="Apple-style-span" face="'Devanagari MT'" size="7"><span class="Apple-style-span" style="font-size: 27px; "><font class="Apple-style-span" size="5"><span class="Apple-style-span" style="font-size: 18px; ">ॐ</span></font></span></font></p></span><p></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; line-height: 19px; font: normal normal normal 16px/normal Helvetica; "><span class="Apple-style-span" style="font-family: 'Lucida Grande'; font-size: 10px; ">Michael Yourshaw</span></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">UCLA Geffen School of Medicine</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Department of Human Genetics, Nelson Lab</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">695 Charles E Young Drive S</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Gonda 5554</span></div><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 3px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Los Angeles CA 90095-8348 USA</span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 3px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; color: rgb(0, 0, 153); "><span style="text-decoration: underline; letter-spacing: 0px; "><a href="mailto:myourshaw@ucla.edu">myourshaw@ucla.edu</a></span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">970.691.8299</span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; font: normal normal normal 9px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">This message is intended only for the use of the addressee and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT. 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