http://genome.sph.umich.edu/w/index.php?action=history&feed=atom&title=830_-_BestAlignment%3A%3AMaqAlignment%28%29 2026-09-28T07:05:02Z Revision history for this page on the wiki MediaWiki 1.43.1 http://genome.sph.umich.edu/w/index.php?title=830_-_BestAlignment::MaqAlignment()&diff=8898&oldid=prev 2013-10-28T17:45:02Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:45, 28 October 2013</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">&lt;source lang="cpp"&gt;</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>void BestAlignment::MaqAlignment(MaqIndex &amp; index1, MaqIndex &amp; index2, MaqIndex &amp; index3, FastQ &amp; read)</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>void BestAlignment::MaqAlignment(MaqIndex &amp; index1, MaqIndex &amp; index2, MaqIndex &amp; index3, FastQ &amp; read)</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l37">Line 37:</td> <td colspan="2" class="diff-lineno">Line 39:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> mapQ = quality &lt; 0.5 ? 0 : (quality &gt; 0.9999999998 ? 99 : (int) (0.5 + 10 * log(1.0 - quality) / log(0.1)));</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> mapQ = quality &lt; 0.5 ? 0 : (quality &gt; 0.9999999998 ? 99 : (int) (0.5 + 10 * log(1.0 - quality) / log(0.1)));</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>}</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>}</div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">&lt;/source&gt;</ins></div></td></tr> </table>

Goncalo http://genome.sph.umich.edu/w/index.php?title=830_-_BestAlignment::MaqAlignment()&diff=8897&oldid=prev 2013-10-28T17:44:35Z

<p>Created page with &quot;void BestAlignment::MaqAlignment(MaqIndex &amp; index1, MaqIndex &amp; index2, MaqIndex &amp; index3, FastQ &amp; read) { position = -1; sumQ = mapQ = 0; mismatches = read.Length(); forwa...&quot;</p> <p><b>New page</b></p><div>void BestAlignment::MaqAlignment(MaqIndex &amp; index1, MaqIndex &amp; index2, MaqIndex &amp; index3, FastQ &amp; read)<br /> {<br /> position = -1;<br /> sumQ = mapQ = 0;<br /> mismatches = read.Length();<br /> forward = true;<br /> <br /> for (unsigned int i = 0; i &lt; read.quality.Length(); i++)<br /> sumQ += read.quality[i];<br /> <br /> mapQdenominator = 0;<br /> <br /> ClearPositions();<br /> EvaluateAlignment(index1, read, 0);<br /> EvaluateAlignment(index1, read, index1.bases);<br /> EvaluateAlignment(index1, read, index1.bases / 2);<br /> EvaluateAlignment(index2, read, 0);<br /> EvaluateAlignment(index2, read, index2.bases / 2);<br /> EvaluateAlignment(index3, read, 0);<br /> <br /> read.Reverse();<br /> <br /> int offset = read.Length() - 24;<br /> <br /> ClearPositions();<br /> EvaluateAlignment(index1, read, offset + 0, false);<br /> EvaluateAlignment(index1, read, offset + index1.bases, false);<br /> EvaluateAlignment(index1, read, offset + index1.bases / 2, false);<br /> EvaluateAlignment(index2, read, offset + 0, false);<br /> EvaluateAlignment(index2, read, offset + index2.bases / 2, false);<br /> EvaluateAlignment(index3, read, offset + 0, false);<br /> <br /> if (forward) read.Reverse();<br /> <br /> double quality = pow(10.0, -0.1 * sumQ) / (mapQdenominator + 1e-30);<br /> <br /> mapQ = quality &lt; 0.5 ? 0 : (quality &gt; 0.9999999998 ? 99 : (int) (0.5 + 10 * log(1.0 - quality) / log(0.1)));<br /> }</div>

Goncalo