<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 class="" 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 class="" style="color:black;white-space:nowrap;margin-left:6px"><tbody><tr style="vertical-align:top"><td class="" 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 class="" 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 class="" 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 class="" style="white-space:pre">      </span>104269332<span class="" style="white-space:pre"> </span>CNV7<span class="" style="white-space:pre">      </span>G<span class="" style="white-space:pre"> </span><DEL><span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>SVTYPE=DEL;END=104278677<br>
</div><div><br></div><div>Any thoughts on that?</div><div><br></div><div>Thanks,</div><div><br></div>-- <br><div dir="ltr">G.</div>
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