<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Thank you very much! :-)<div><br><div style=""><div>On 23 Feb 2015, at 11:13, Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Hi Catherine,<div><br></div><div>Yes, you can increase the number by editing and recompiling the C code used to calculate the LD values:</div><div><br></div><div>(/path/to/src/ is where you have the ensembl-variation API module).</div><div><br></div><div>cd /path/to/src/ensembl-variation/C_code</div><div>sed -i.bak "s/#define SIZE 250/#define SIZE 500/" calc_genotypes.c<br></div><div>make</div><div><br></div><div>You then have to either copy the resultant calc_genotypes file somewhere in your path, or add the path to your PATH environment variable</div><div><br></div><div>export PATH=/path/to/src/ensembl-variation/C_code:${PATH}<br></div><div><br></div><div>if you use BASH, or</div><div><br></div><div>setenv PATH /path/to/src/ensembl-variation/C_code:${PATH}</div><div><br></div><div>if you use tcsh or csh.</div><div><br></div><div>If you re-run your script it should then use the recompiled binary.</div><div><br></div><div>HTH</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 23 February 2015 at 10:15, Catherine Leroy <span dir="ltr"><<a href="mailto:cleroy@ebi.ac.uk" target="_blank">cleroy@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hello, <div><br></div><div>Me again! Again on LD. </div><div><br></div><div>I’m still trying to get for : </div><div><span style="white-space:pre-wrap"> </span>snp : <span style="background-color:rgb(255,255,255)">rs11010067</span></div><div>all the LD r2 values. </div><div><br></div><div>If I use population : <span style="background-color:rgb(255,255,255)">1000GENOMES:phase_1_EUR</span></div><div>I get the following message : </div><div><div style="margin:0px">Number of genotypes supported by the program (250) exceeded</div></div><div style="margin:0px"><br></div><div style="margin:0px">I can work around that using population : </div><div style="margin:0px"><pre style="background-color:rgb(255,255,255)"><font face="Helvetica">1000GENOMES:phase_1_GBR</font></pre><div>which is a sub population of <span style="background-color:rgb(255,255,255)">1000GENOMES:phase_1_EUR. </span></div><div><span style="background-color:rgb(255,255,255)"><br></span></div><div><span style="background-color:rgb(255,255,255)">Is there any way I can increase the 250 limit to be able to use </span><span style="background-color:rgb(255,255,255)">1000GENOMES:phase_1_EUR? As this would be probably more representative then the sub population?</span></div><div><span style="background-color:rgb(255,255,255)"><br></span></div><div><span style="background-color:rgb(255,255,255)">Thanks for your help,</span></div><div><span style="background-color:rgb(255,255,255)">Catherine</span></div></div></div><br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br></div>
_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote></div><br></div></body></html>