<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Hi Wallace,</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Thanks for finding this and getting to the root of the problem. I’ve patched a fix to the plugin on the dev and release/89 branches.</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="margin: 0px;"><a href="https://github.com/Ensembl/VEP_plugins/commit/cb2bb3230320c704a0786604617c626f16a88423">https://github.com/Ensembl/VEP_plugins/commit/cb2bb3230320c704a0786604617c626f16a88423</a></div><div id="bloop_customfont" style="margin: 0px;"><br></div><div id="bloop_customfont" style="margin: 0px;">Regards</div><div id="bloop_customfont" style="margin: 0px;"><br></div><div id="bloop_customfont" style="margin: 0px;">Will McLaren</div><div id="bloop_customfont" style="margin: 0px;">Ensembl Variation</div> <br> <div id="bloop_sign_1498465892793714944" class="bloop_sign"></div> <br><p class="airmail_on">On 26 June 2017 at 04:48:06, Wallace Ko (<a href="mailto:myko@l3-bioinfo.com">myko@l3-bioinfo.com</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div><div></div><div>
<title></title>
<div dir="ltr">Hi,
<div><br></div>
<div>It is observed that the GeneSplicer plugin is only returning
results for first result of the same variant.</div>
<div><br></div>
<div>It is caused by updated cache:</div>
<div>
<ol>
<li>The methods <font face="monospace, monospace">results_from_cache</font> and <font face="monospace, monospace">results_from_seq</font> return <a href="https://github.com/Ensembl/VEP_plugins/blob/b25f865c97a30ffdca18f63040f715032578ea8a/GeneSplicer.pm#L186-L187">
an array of hash</a>.</li>
<li>The method <font face="monospace, monospace">compare_results</font> returns <a href="https://github.com/Ensembl/VEP_plugins/blob/b25f865c97a30ffdca18f63040f715032578ea8a/GeneSplicer.pm#L190-L191">
the array (<font face="monospace, monospace">lost</font> and
<font face="monospace, monospace">diff</font>) that contains same
hashes</a> (for case of diff, it <a href="https://github.com/Ensembl/VEP_plugins/blob/b25f865c97a30ffdca18f63040f715032578ea8a/GeneSplicer.pm#L332-L334">
modifies</a> score and confidence of hash in first array).</li>
<li>When <a href="https://github.com/Ensembl/VEP_plugins/blob/b25f865c97a30ffdca18f63040f715032578ea8a/GeneSplicer.pm#L220">
formatting result</a>, the <font face="monospace, monospace">map_ss_coords</font> method modifies the
<font face="monospace, monospace">end5</font> and <font face="monospace, monospace">end3</font> property of the cache. The cache
now contains translated positions. Subsequent runs of the plugin on
the same sequence grep overlapping results using the translated
positions and thus no result is returned.</li>
</ol>
<div>The quick fix I am using is to deep clone the values returned
from <font face="monospace, monospace">results_from_cache</font> and <font face="monospace, monospace">results_from_seq</font>.</div>
</div>
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<div>
<div class="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr"><span>Regards,<br>
Wallace Ko<br></span></div>
<div><span>L3 Bioinformatics<br></span></div>
</div>
</div>
</div>
</div>
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