<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Dave,<div><br></div><div>I have since realised that this is actually not a new problem. It seems that the alignments in the details page <span class="Apple-style-span" style="text-decoration: underline;">have never indicated mismatch</span> by dropping the '|' only insertions and deletions.<br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="font-size: 12px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br class="Apple-interchange-newline">Keiran</div></div></span></div></span></span><br class="Apple-interchange-newline"></span></span> </div><br><div><div>On 19 Feb 2010, at 19:08, Dave Clements, GMOD Help Desk wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Keiran,<div><br></div><div>Are you still seeing this problem?</div><div><br></div><div>Thanks,</div><div><br></div><div>Dave C<br><br><div class="gmail_quote">On Mon, Feb 15, 2010 at 9:06 AM, Keiran Raine <span dir="ltr"><<a href="mailto:kr2@sanger.ac.uk">kr2@sanger.ac.uk</a>></span> wrote:<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi,<br> <br> It appears that the aligned sequence given in the default link for an individual read has stopped indicating where mismatches occur.<br> <br> This appears to have started when I upgraded to the SVN version of Bio::DB::Sam to fix another issue.<br><font color="#888888"> <br> <br> <br> -- <br> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a charity registered in England with number 1021457 and acompany registered in England with number 2742969, whose registeredoffice is 215 Euston Road, London, NW1 2BE.<br> </font><br><br> <br> Regards,<br> <br> Keiran Raine<br> Senior Computer Biologist<br> The Cancer Genome Project<br> Ext: 2100<br> <a href="mailto:kr2@sanger.ac.uk" target="_blank">kr2@sanger.ac.uk</a><br> <br> The Wellcome Trust Sanger Institute is operated by Genome Research<br> Limited, a charity registered in England with number 1021457 and a<br> company registered in England with number 2742969, whose registered<br> office is 215 Euston Road, London, NW1 2BE.<br> <br> <br> <br> <br>------------------------------------------------------------------------------<br> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,<br> Predictive Self Healing and Award Winning ZFS. 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--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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