<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;"><br></div> <br> <div id="bloop_sign_1500278412836910080" class="bloop_sign"></div> <br><p class="airmail_on">On 15 July 2017 at 01:25:30, João Eiras (<a href="mailto:joao.eiras@gmail.com">joao.eiras@gmail.com</a>) wrote:</p> <div><blockquote type="cite" class="clean_bq" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"><span><div><div></div><div>On 14 July 2017 at 15:38, William McLaren <wm2@ebi.ac.uk> wrote:<br>> As the documentation for -minimal mentions you should use -allele_number to<br>> track alleles from input to output.<br>><br><br>Can I suggest --minimal implying --allele_num ? Or rather, I think<br>allele_num should always be enabled since it's much more reliable that<br>trying to parse "variant_allele" or "codons"</div></div></span></blockquote></div><p><br></p><p>Agreed; -minimal will switch on -allele_number in release/90.</p><p><br></p><div><div><blockquote type="cite" class="clean_bq" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"><span><div><div><br><br>> As you note for your example the ALT will be “-“ in all cases, but the<br>> start/end coordinates used to calculate the consequences will be different.<br>><br>> It’s a matter of opinion unfortunately whether -minimal should be the<br>> default or not; we err on the side of trying not to confuse users too much<br>> by making it not the default. It’s something that could be up for<br>> consideration for change in the future, though.<br><br>That's fine by me, and I do think the output should resemble the input<br>as much as possible.<br><br>However, stripping the ref or not should NOT affect the result of the<br>annotation.</div></div></span></blockquote></div><p>Agreed again, but unfortunately this is not as straightforward in practice as it sounds in principle.</p><p>It is something we’re working on for the future.</p><p>Regards</p><p>Will</p><div><blockquote type="cite" class="clean_bq" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"><span><div><div><br><br>Thank you so much for your time !<br>_______________________________________________<br>Dev mailing list Dev@ensembl.org<br>Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev<br>Ensembl Blog: http://www.ensembl.info/<br></div></div></span></blockquote></div></div></body></html>