<div dir="ltr">Hi,<div><br></div><div>Thanks Genomeo for bringing this up seems like an important issue. Ensembl folks, could you please clarify whether Structural variants are processed by the plugin by default or whether the variant_feature_types is required?</div>

<div><br></div><div>Cheers,</div><div><br></div><div>Mike<br><div class="gmail_extra"><br><br><div class="gmail_quote">On 20 June 2014 18:25, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hi Will/others,<div><br></div><div>TSSDistance.pm currently does not seem to consider structural variants. Based on this doxygen documentation:</div>

<div><br></div><div><div style="font-size:11.818181991577148px;font-family:'Lucida Grande',Verdana,Geneva,Arial,sans-serif;color:rgb(37,53,85);border-top-width:1px;border-top-style:solid;border-top-color:rgb(168,184,217);border-left-width:1px;border-left-style:solid;border-left-color:rgb(168,184,217);border-right-width:1px;border-right-style:solid;border-right-color:rgb(168,184,217);padding:6px 0px;font-weight:bold;border-top-right-radius:8px;border-top-left-radius:8px;background-image:url(http://static.ensembl.org/info/docs/Doxygen/compara-api/nav_f.png);background-color:rgb(226,232,242);background-repeat:repeat-x">


<table style="color:black;white-space:nowrap;margin-left:6px"><tbody><tr style="vertical-align:top"><td style="font-size:1em;border:0px;color:rgb(51,51,51);margin-left:6px">public Listref Bio::EnsEMBL::Variation::Utils::BaseVepPlugin::variant_feature_types</td>


<td style="font-size:1em;border:0px;color:rgb(51,51,51)">(</td><td style="font-size:1em;border:0px;color:rgb(96,32,32)"></td><td style="font-size:1em;border:0px;color:rgb(51,51,51)">)</td><td style="font-size:1em;border:0px;color:rgb(51,51,51)">


</td></tr></tbody></table></div><div style="font-size:11.818181991577148px;font-family:'Lucida Grande',Verdana,Geneva,Arial,sans-serif;color:rgb(0,0,0);border-width:0px 1px 1px;border-bottom-style:solid;border-bottom-color:rgb(168,184,217);border-left-style:solid;border-left-color:rgb(168,184,217);border-right-style:solid;border-right-color:rgb(168,184,217);padding:2px 5px;border-bottom-left-radius:8px;border-bottom-right-radius:8px;background-color:rgb(251,252,253)">


<pre style="font-family:'Courier New',Courier,monospace;font-size:1em;margin-top:0px;margin-bottom:16px;line-height:16px">  Description: To indicate which types of variation features a plugin is interested
               in, plugins should return a listref of the types of variation feature 
               they can deal with. Currently this list should include one or more of: 
               'VariationFeature' or 'StructuralVariationFeature' 
  Returntype : listref
  Status     : Experimental</pre></div><div><br></div><div>I tried adding the following code at the top of the plugin:</div><div><br></div><div><div>sub variant_feature_types {</div><div>    return [<span style="color:rgb(0,0,0);font-family:'Courier New',Courier,monospace;font-size:1em;line-height:16px">'Variation','</span>StructuralVariation'];</div>


<div>}</div></div><div><br></div><div>but it does not work.  This is the input in VCF:</div><div>5<span style="white-space:pre-wrap">    </span>104269332<span style="white-space:pre-wrap">       </span>CNV7<span style="white-space:pre-wrap">    </span>G<span style="white-space:pre-wrap">       </span><DEL><span style="white-space:pre-wrap">     </span>.<span style="white-space:pre-wrap">       </span>PASS<span style="white-space:pre-wrap">    </span>SVTYPE=DEL;END=104278677<br>


</div><div><br></div><div>Any thoughts on that?</div><div><br></div><div>Thanks,</div><span><font color="#888888"><div><br></div>-- <br><div dir="ltr">G.</div>
</font></span></div></div></blockquote></div></div></div></div>