<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 uninitialized value errors in VEP.pm and ignored tructural_variation_overlaps.<div><br></div><div>Examples of offending input VCF files are attached.</div><div><br></div><div>test_ab.vcf has two records, the second of which causes uninitialized value errors.</div><div><br></div><div>test_b.VCF has only the uninitialized value error-causing record. The problem here is that we don’t see the uninitialized value errors because the structural_variation_overlaps are being ignored (incorrectly or by design?).</div><div><br></div><div>Note that the uninitialized value errors occur when both records are present but not if either one is by itself in a one-record VCF.</div><div><br></div><div>The uninitialized value errors are associated with the 22<span class="Apple-tab-span" style="white-space:pre"> </span>22569659<span class="Apple-tab-span" style="white-space:pre"> </span>MERGED_DEL_2_105175 record, which is processed first by get_all_consequences.</div><div><br></div><div>Errors:</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/Utils/VariationEffect.pm line 111, <GEN9> line 34.</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Use of uninitialized value in pattern match (m//) at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 111, <GEN9> line 34.</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/Utils/VariationEffect.pm line 121, <GEN9> line 34.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Use of uninitialized value in pattern match (m//) at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 121, <GEN9> line 34.</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/Utils/VariationEffect.pm line 131, <GEN9> line 34.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Use of uninitialized value in pattern match (m//) at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 131, <GEN9> line 34.</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/Utils/VariationEffect.pm line 142, <GEN9> line 34.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Use of uninitialized value in pattern match (m//) at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 142, <GEN9> line 34.</div><div><br></div><div><br></div><div>The problem causing the uninitialized value errors is that $bvfoa->base_variation_feature->class_SO_term is undef.</div><div><br></div><div>The problem causing the code that generates the errors not to be executed when there is only one record in the VCF is:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at VEP.pm whole_genome_fetch_sv line 2250</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>if(defined($tr_cache->{$chr})) {</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>When there is one variant in the VCF file, $tr_cache has no contents, and the code that pushes $svf->{structural_variation_overlaps} is not executed.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>When two variants are in the VCF file, $tr_cache has 6 transcripts under chr 22, the structural_variation_overlaps get pushed, and eventually the uninitialized value errors are emitted.</div><div><br></div><div></div></body></html>