<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Anja,<div class=""><br class=""></div><div class="">Thanks for the quick fix. After pull'ing my checkout of the 93 branch, I no longer see the error and I seem to get good LD results. But it seems like the Tabix.pm query method no longer gets called in the same way? That is, the debug code I put in that function doesn't seem to get called anymore, so I can't positively confirm what region has been sent to the function. Was there some change, such that Tabix.pm->query no longer gets called?</div><div class=""><br class=""></div><div class="">Thanks.</div><div class=""><br class=""></div><div class="">Best,</div><div class=""><br class=""></div><div class="">Andrew</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Sep 13, 2018, at 2:24 AM, Anja Thormann <<a href="mailto:anja@ebi.ac.uk" class="">anja@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Andrew,<div class=""><br class=""></div><div class="">this has been fixed on release/93 branch. We pushed the <a href="https://github.com/Ensembl/ensembl-variation/pull/226" class="">code fix </a>to the release/93 branch. Please refresh your checkout and let us know if you encounter any problems with the code. Thank you for reporting the error.</div><div class=""><br class=""></div><div class="">Best wishes,</div><div class="">Anja<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On 11 Sep 2018, at 17:09, Anja Thormann <<a href="mailto:anja@ebi.ac.uk" class="">anja@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Andrew,<br class=""><br class="">thank you for the bug report. We are looking into what’s causing the error and will soon get back to you with a fix.<br class=""><br class="">Thank you,<br class="">Anja<br class=""><br class=""><blockquote type="cite" class="">On 10 Sep 2018, at 09:08, <a href="mailto:andrew126@mac.com" class="">andrew126@mac.com</a> wrote:<br class=""><br class="">Hi,<br class=""><br class="">This applies to Ensembl API v93.<br class=""><br class="">I am occassionally getting failures from ldFeatureContainerAdaptor->fetch_by_VariationFeature with the following message:<br class=""><br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>You must specify a region in the format chr, chr:start or chr:start-end at /usr/local/ensembl/ak_API93/Bio-DB-HTS/lib/Bio/DB/HTS/Tabix.pm line 104.<br class=""><br class="">One of the failure instances occured for variation feature rs12445289 (its chr 16 mapping), and I was able to see that this region was provided to Tabix.pm:<br class=""><br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>16:-81648-918353<br class=""><br class="">rs12445289 is at location 418,353 on chr 16, and I was using a max_snp_distance of 500000, which seems to explain the start and end values sent to Tabix, but Tabix.pm does not seem prepared to handle a negative start position (I think it wants to see only a digit after the first colon).<br class=""><br class="">fetch_by_VariationFeature for chr-16 rs12445289 +/- 500,000 does not fail throw any error for Ensembl API v90, fwiw<br class=""><br class="">Is there a fix possible for this?<br class=""><br class="">Thanks for any help.<br class=""><br class="">Best,<br class=""><br class="">Andrew<br class=""><br class=""><br class=""><br class="">_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></blockquote><br class="">_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></div></blockquote></div><br class=""></div></div>_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></blockquote></div><br class=""></div></body></html>