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<p class="MsoNormal"><span style="font-size:11.0pt">Hi Magali,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you very much, please keep us posted!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Daniel<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">Dev <dev-bounces@ensembl.org> on behalf of mag <mr6@ebi.ac.uk><br>
<b>Reply-To: </b>Ensembl developers list <dev@ensembl.org><br>
<b>Date: </b>Friday, 16 June 2017 at 14:56<br>
<b>To: </b>"dev@ensembl.org" <dev@ensembl.org><br>
<b>Subject: </b>Re: [ensembl-dev] REST - map endpoint</span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Dear Daniel,<br>
<br>
Thank you for reporting this, it is definitely not expected behaviour.<br>
We will investigate the problem and let you know when a fix is available.<br>
<br>
<br>
Kind regards,<br>
Magali<o:p></o:p></p>
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<p class="MsoNormal">On 16/06/2017 13:50, Daniel Suveges wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Ok, I have to adjust my question: apparently sometimes the query returns the expected coordinates, but mostly the return is empty. I hope this helps.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">(On the attached screenshot you can see that the response to the same query sometimes empty, sometimes not.)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Best,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Daniel</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">Dev
<a href="mailto:dev-bounces@ensembl.org"><dev-bounces@ensembl.org></a> on behalf of Daniel Suveges
<a href="mailto:ds26@sanger.ac.uk"><ds26@sanger.ac.uk></a><br>
<b>Reply-To: </b>Ensembl developers list <a href="mailto:dev@ensembl.org"><dev@ensembl.org></a><br>
<b>Date: </b>Friday, 16 June 2017 at 13:16<br>
<b>To: </b>Ensembl developers list <a href="mailto:dev@ensembl.org"><dev@ensembl.org></a><br>
<b>Subject: </b>[ensembl-dev] REST - map endpoint</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Times New Roman","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Hi Guys,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">I’m trying to use the map endpoint of the REST service (to map between the human GRCh37 and 38 build) and I’m encountering some unexpected behavior:</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Let’s take the variant rs11553699 for example:
</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">it’s GRCh37 coordinates:
</span><span style="font-size:11.0pt">12:122216910</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">it’s GRCh38 coordinates:
</span><span style="font-size:11.0pt">12:121779004</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">If I want to map it’s GRCh37 coordinates to the newer build it works:</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><a href="http://rest.ensembl.org/map/human/GRCh37/12:122216910..122216910:1/GRCh38?content-type=application/json">http://rest.ensembl.org/map/human/GRCh37/12:122216910..122216910:1/GRCh38?content-type=application/json</a></span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">But when I’m trying to do the same in the opposite direction, the ‘mappings’ array is empty in the returned json:</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><a href="http://rest.ensembl.org/map/human/GRCh38/12:121779004..121779004:1/GRCh37?content-type=application/json">http://rest.ensembl.org/map/human/GRCh38/12:121779004..121779004:1/GRCh37?content-type=application/json</a></span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">For other GRCh38 coordinates mapping works, this position has coordinates in both build, so it is not clear to me why the second query seemingly fails.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Thank you very much for your help!</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Best,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Daniel</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-GB"><br>
<br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
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<pre>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></pre>
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<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-GB"><br>
<br>
<o:p></o:p></span></p>
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