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GitLab

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<h3>

Andreas Tille pushed to branch master

at <a href="https://salsa.debian.org/med-team/kineticstools">Debian Med / kineticstools</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/51529735ad6e3f3b5d154b125215fa5607f0b4a0">51529735</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2020-04-22T22:11:37+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove non-free documentation from source tarball

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/e34aa1ece64a6d13a97efb79a788b22baddd4bb4">e34aa1ec</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2020-04-22T22:12:14+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove outdated README.source

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/74479cd38e636f36bb65890f956c81044366eb78">74479cd3</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2020-04-22T22:12:34+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.6.1+git20200325.3558942+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/42bb05bed6c47aaa9b078a9b1ad7595586bc3b98">42bb05be</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2020-04-22T22:12:49+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.6.1+git20200325.3558942+dfsg'

Update to upstream version '0.6.1+git20200325.3558942+dfsg'

with Debian dir 847fb30adc022a60e0b486c55b1a110cfd04049d</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/dd70c05e15ea44c9779a2492d69df09eff82f802">dd70c05e</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2020-04-22T22:16:53+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>10 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">

<span class="deleted-file">

−

debian/README.source

</span>

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">

debian/copyright

</a>

</li>

<li class="file-stats">

<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">

debian/watch

</a>

</li>

<li class="file-stats">

<a href="#bd840b86ad7e4d94e511deee119e3adadf456f9e">

<span class="deleted-file">

−

doc/whitepaper/ecoli-roc.png

</span>

</a>

</li>

<li class="file-stats">

<a href="#621157f347c580467214788d15c83bda9c5c6573">

<span class="deleted-file">

−

doc/whitepaper/kinetics.bib

</span>

</a>

</li>

<li class="file-stats">

<a href="#687366fd7c1064e966e259dad044c16d93fc760b">

<span class="deleted-file">

−

doc/whitepaper/kinetics.pdf

</span>

</a>

</li>

<li class="file-stats">

<a href="#14b481c1742d1fb421e1e8dfdd7e4ceb246d32f4">

<span class="deleted-file">

−

doc/whitepaper/kinetics.tex

</span>

</a>

</li>

<li class="file-stats">

<a href="#9d2b806666f22ae8409c0c1ec8e67b10464bd88d">

<span class="deleted-file">

−

doc/whitepaper/logo.jpg

</span>

</a>

</li>

<li class="file-stats">

<a href="#04273637b399088c73b6442fb97878fc52855ec7">

<span class="deleted-file">

−

doc/whitepaper/position-influence.png

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="cf9802e192b48f765b1b5c8268d550d89c933053">

<a href="https://salsa.debian.org/med-team/kineticstools/-/compare/10b4eeb36249db8e1ffc24a6e7aa0f12ffbe2ca6...dd70c05e15ea44c9779a2492d69df09eff82f802#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong>

deleted

</a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">kineticstools for Debian</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">-------------------------------</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Importing New Upstream Releases</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">===============================</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Since upstream has ignored the request to tag releases [1], we use the</span>

</pre>

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8

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">following approach to retrieve the upstream source.</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">* Use the upstream Git annotations for setup.py [2] to find the commit that</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">  updates the version string.</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">* Download the tarball corresponding to that commit.</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">* Update the version accordingly in debian/changelog</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">* run mk-origtargz on the downloaded tarball in order to repack the tarball</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">  and remove non-DFSG files (declared in debian/copyright)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"></span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">1. https://github.com/PacificBiosciences/kineticsTools/issues/49</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">2. https://github.com/PacificBiosciences/kineticsTools/blame/master/setup.py</span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> -- Afif Elghraoui <afif@debian.org>, Sun, 15 Jan 2017 12:35:59 -0800</span>

</pre>

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22

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"></span></pre>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/kineticstools/-/compare/10b4eeb36249db8e1ffc24a6e7aa0f12ffbe2ca6...dd70c05e15ea44c9779a2492d69df09eff82f802#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">kineticstools (0.6.1+git20200325.3558942<span class="idiff left right">-2) UNRELEASED</span>; urgency=medium</span>

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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kineticstools (0.6.1+git20200325.3558942<span class="idiff left right">+dfsg-1) unstable</span>; urgency=medium</span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">  [ Etienne Mollier ]</span>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">  * minor d/rules update to make commands independent of minor python version</span>

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> -- Etienne Mollier <etienne.mollier@mailoo.org>  Wed, 22 Apr 2020 21:07:00 +0200</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  [ Andreas Tille ]</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  * Remove non-free documentation from source tarball</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">    Closes: #958471</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">  * Remove outdated README.source</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Wed, 22 Apr 2020 22:14:02 +0200</span>

</pre>

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7

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">kineticstools (0.6.1+git20200325.3558942-1) unstable; urgency=medium</span>

</pre>

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9

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14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>

</pre>

</td>

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<br>

</li>

<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<a href="https://salsa.debian.org/med-team/kineticstools/-/compare/10b4eeb36249db8e1ffc24a6e7aa0f12ffbe2ca6...dd70c05e15ea44c9779a2492d69df09eff82f802#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</td>

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2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: kineticsTools</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Upstream-Contact: devnet@pacificbiosciences.com</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Source: https://github.com/PacificBiosciences/kineticsTools</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Files-Excluded: */whitepaper</span>

</pre>

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5

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>

</pre>

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6

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7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Files: *</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Copyright:</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">

<a href="https://salsa.debian.org/med-team/kineticstools/-/compare/10b4eeb36249db8e1ffc24a6e7aa0f12ffbe2ca6...dd70c05e15ea44c9779a2492d69df09eff82f802#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>

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1

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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">opts="mode=git,pretty=0.6.1+git%cd.%h" \</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts="<span class="idiff left right">repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz,</span>mode=git,pretty=0.6.1+git%cd.%h" \</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">    https://github.com/PacificBiosciences/kineticsTools.git HEAD</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>

</pre>

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6

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"># Issue asking for release tags:</span>

</pre>

</td>

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<br>

</li>

<li id="bd840b86ad7e4d94e511deee119e3adadf456f9e">

<a href="https://salsa.debian.org/med-team/kineticstools/-/compare/10b4eeb36249db8e1ffc24a6e7aa0f12ffbe2ca6...dd70c05e15ea44c9779a2492d69df09eff82f802#bd840b86ad7e4d94e511deee119e3adadf456f9e"><strong>doc/whitepaper/ecoli-roc.png</strong>

deleted

</a>

<hr>

No preview for this file type

<br>

</li>

<li id="621157f347c580467214788d15c83bda9c5c6573">

<a href="https://salsa.debian.org/med-team/kineticstools/-/compare/10b4eeb36249db8e1ffc24a6e7aa0f12ffbe2ca6...dd70c05e15ea44c9779a2492d69df09eff82f802#621157f347c580467214788d15c83bda9c5c6573"><strong>doc/whitepaper/kinetics.bib</strong>

deleted

</a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">@article{ forney1973viterbi,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">  title={The viterbi algorithm},</span>

</pre>

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3

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">  author={Forney Jr, G.D.},</span>

</pre>

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4

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</td>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">  journal={Proceedings of the IEEE},</span>

</pre>

</td>

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5

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">  volume={61},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">  number={3},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

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</td>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">  pages={268--278},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">  year={1973},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">  publisher={IEEE}</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">}</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">@article{ flusberg2010direct,</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">  title={Direct detection of DNA methylation during single-molecule, real-time sequencing},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">  author={Flusberg, B.A. and Webster, D.R. and Lee, J.H. and Travers, K.J. and Olivares, E.C. and Clark, T.A. and Korlach, J. and Turner, S.W.},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">  journal={Nature methods},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">  volume={7},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">  number={6},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">  pages={461--465},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">  year={2010},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">  publisher={Nature Publishing Group}</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">}</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

22

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

23

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">@article{ eid2009real,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">  title={Real-time DNA sequencing from single polymerase molecules},</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

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</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">  author={Eid, J. and Fehr, A. and Gray, J. and Luong, K. and Lyle, J. and Otto, G. and Peluso, P. and Rank, D. and Baybayan, P. and Bettman, B. and others},</span>

</pre>

</td>

</tr>

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</td>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">  journal={Science},</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">  volume={323},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">  number={5910},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">  pages={133--138},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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</td>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">  year={2009},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">  publisher={American Association for the Advancement of Science}</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">}</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">@article{ clark2012characterization,</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">  title={Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">  author={Clark, T.A. and Murray, I.A. and Morgan, R.D. and Kislyuk, A.O. and Spittle, K.E. and Boitano, M. and Fomenkov, A. and Roberts, R.J. and Korlach, J.},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

37

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</td>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">  journal={Nucleic Acids Research},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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</td>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">  volume={40},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

39

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</td>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">  number={4},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

40

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">  pages={e29--e29},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">  year={2012},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">  publisher={Oxford Univ Press}</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">}</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

44

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

45

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">@Article{ blasr, </span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

46

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">AUTHOR = {Chaisson, Mark and Tesler, Glenn},</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

47

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">TITLE = {Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application},</span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">JOURNAL = {BMC Bioinformatics},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">VOLUME = {13},</span>

</pre>

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50

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">YEAR = {2012},</span>

</pre>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">NUMBER = {1},</span>

</pre>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">PAGES = {238},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">URL = {http://www.biomedcentral.com/1471-2105/13/238},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">DOI = {10.1186/1471-2105-13-238},</span>

</pre>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">ISSN = {1471-2105},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">ABSTRACT = {We describe the method BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion error. We also present a combinatorial model of sequencing error that motivates why our approach is effective. The results indicate that mapping SMS reads is both highly specific and rapid.},</span>

</pre>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">}</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"></span>

</pre>

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</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">@book{ cart,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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</td>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">author = "L. Breiman and J. H. Friedman and R. Olshen and C. J. Stone",</span>

</pre>

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</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">title = "Classification and Regression Trees",</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">publisher = "Wadsworth",</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">address = "Belmont, California",</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">year = "1984"</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">}</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">@article{ gradientboost,</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext">   AUTHOR="Jerome H. Friedman",</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">   TITLE="Greedy Function Approximation: A Gradient Boosting Machine",</span>

</pre>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext">   JOURNAL="The Annals of Statistics",</span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">   YEAR="2001",</span>

</pre>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext">  VOLUME="29",</span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext">  PAGES="1189-1232"</span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">}</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">@article{ crf-boost,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">  AUTHOR= "Thomas G. Dietterich, Adam Ashenfelter, and Yaroslav Bulatov",</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">  TITLE="Training Conditional Random Fields via Gradient Tree Boosting",</span>

</pre>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">  JOURNAL="International Conference on Machine Learning",</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">  YEAR="2004",</span>

</pre>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">  VOLUME="1",</span>

</pre>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">  PAGES="1-2"</span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">}</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">@Manual{ gbm,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext">  title = {gbm: Generalized Boosted Regression Models},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">  author = {Greg Ridgeway},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">  year = {2010},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">  note = {R package version 1.6-3.1},</span>

</pre>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">  url = {http://CRAN.R-project.org/package=gbm},</span>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">}</span></pre>

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<li id="687366fd7c1064e966e259dad044c16d93fc760b">

<a href="https://salsa.debian.org/med-team/kineticstools/-/compare/10b4eeb36249db8e1ffc24a6e7aa0f12ffbe2ca6...dd70c05e15ea44c9779a2492d69df09eff82f802#687366fd7c1064e966e259dad044c16d93fc760b"><strong>doc/whitepaper/kinetics.pdf</strong>

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<li id="14b481c1742d1fb421e1e8dfdd7e4ceb246d32f4">

<a href="https://salsa.debian.org/med-team/kineticstools/-/compare/10b4eeb36249db8e1ffc24a6e7aa0f12ffbe2ca6...dd70c05e15ea44c9779a2492d69df09eff82f802#14b481c1742d1fb421e1e8dfdd7e4ceb246d32f4"><strong>doc/whitepaper/kinetics.tex</strong>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="tex"><span class="k" style="font-weight: 600;">\documentclass</span><span class="na" style="color: #008080;">[pdftex]</span><span class="p">{</span>article<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="tex"><span class="k" style="font-weight: 600;">\usepackage</span><span class="p">{</span>float<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="tex"><span class="k" style="font-weight: 600;">\usepackage</span><span class="p">{</span>graphicx<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="tex"><span class="k" style="font-weight: 600;">\usepackage</span><span class="p">{</span>hyperref<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="tex"><span class="k" style="font-weight: 600;">\usepackage</span><span class="p">{</span>amsmath<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="tex"><span class="k" style="font-weight: 600;">\DeclareMathOperator*</span><span class="p">{</span><span class="k" style="font-weight: 600;">\argmax</span><span class="p">}{</span>argmax<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="tex"><span class="k" style="font-weight: 600;">\newcommand</span><span class="p">{</span><span class="k" style="font-weight: 600;">\mC</span><span class="p">}</span>[1]<span class="p">{$^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m#</span><span class="m" style="color: #099;">1</span><span class="p">}$</span>C<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="tex"><span class="k" style="font-weight: 600;">\newcommand</span><span class="p">{</span><span class="k" style="font-weight: 600;">\mA</span><span class="p">}{$^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">6</span><span class="p">}$</span>A<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="tex"><span class="k" style="font-weight: 600;">\oddsidemargin</span>  0.0in <span class="k" style="font-weight: 600;">\evensidemargin</span> 0.0in</span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="tex"><span class="k" style="font-weight: 600;">\textwidth</span>      6in</span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{document}</span></span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="tex"><span class="k" style="font-weight: 600;">\title</span><span class="p">{</span><span class="nt" style="color: #000080;">\begin{center}</span><span class="k" style="font-weight: 600;">\includegraphics</span><span class="na" style="color: #008080;">[width=2in]</span><span class="p">{</span>logo.jpg<span class="p">}</span><span class="nt" style="color: #000080;">\end{center}</span><span class="k" style="font-weight: 600;">\vspace</span><span class="p">{</span>0.5cm<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="tex">Detection and Identification of Base Modifications with Single Molecule Real-Time Sequencing Data<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="tex"><span class="k" style="font-weight: 600;">\author</span><span class="p">{</span>Patrick Marks, Onureena Banerjee, David Alexander<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="tex"><span class="k" style="font-weight: 600;">\maketitle</span></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">% Will say the section an page</span></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="tex"><span class="k" style="font-weight: 600;">\pagestyle</span><span class="p">{</span>headings<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="tex"><span class="k" style="font-weight: 600;">\section</span><span class="p">{</span>Introduction<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="tex">Single Molecule Real-Time (SMRT<span class="k" style="font-weight: 600;">\textsuperscript</span><span class="p">{</span><span class="k" style="font-weight: 600;">\textregistered</span><span class="p">}</span>) DNA sequencing<span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>eid2009real<span class="p">}</span> data contains information about DNA base modifications imprinted in the kinetics of the polymerization reaction<span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>flusberg2010direct<span class="p">}</span>.  This data enables single-base resolution detection of <span class="k" style="font-weight: 600;">\mA</span>, <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>4<span class="p">}</span>, and <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>5<span class="p">}</span><span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>clark2012characterization<span class="p">}</span>. We discuss the statistical approaches to the detection and identification of DNA modifications from SMRT sequencing data.  Our implementation is available at <span class="k" style="font-weight: 600;">\url</span><span class="p">{</span>http://github.com/PacificBiosciences/kineticsTools<span class="p">}</span>.</span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="tex"><span class="k" style="font-weight: 600;">\section</span><span class="p">{</span>Preparation of IPD data<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="tex"><span class="k" style="font-weight: 600;">\label</span><span class="p">{</span>sec:prep<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="tex">This analysis assumes that we are interested in locus-specific DNA modifications - that is, samples where the same modification is present at a given locus, in some fraction of the sample molecules.  </span>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="tex">We compute a vector of IPDs that map confidently to a given genomic location. We use the alignment tool BLASR <span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>blasr<span class="p">}</span> to generate alignments between reads and a reference template.   BLASR maps each read to the reference sequence. BLASR generates a Mapping QV representing the confidence that the read maps uniquely to the selected genomic interval.  Reads falling within repeats will have a low Mapping QV and are removed from the analysis to prevent incorrect modification calls inside repeats due to mismapped reads.</span>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="tex">Sequencing errors in SMRT sequence data are predominately indels, which causes some ambiguity in the local placement of IPDs to genomic positions.  To avoid most of these errors we only use IPDs if the SMRT sequence matches exactly for <span class="p">$</span><span class="nb" style="color: #0086b3;">k</span><span class="p">$</span> bases around observed base. Currently we use <span class="p">$</span><span class="nb" style="color: #0086b3;">k</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">1</span><span class="p">$</span>.</span>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="tex">These filtering steps yield a vector of IPDs confidently assigned to each genomic position.</span>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="tex">The distribution of IPDs observed at a genomic location is roughly exponential, with a long tail caused by polymerase pausing inherent to SMRT sequencing. Information about base modifications is contained in the main distribution, while the contaminating pauses just contribute noise.  We employ a simple capping procedure to reduce the influence of these outliers: </span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="tex"><span class="p">$</span><span class="nb" style="color: #0086b3;">I</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i</span><span class="p">^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">l</span><span class="o" style="font-weight: 600;">)</span><span class="p">}</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\min</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">R</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i</span><span class="p">^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">l</span><span class="o" style="font-weight: 600;">)</span><span class="p">}</span><span class="nb" style="color: #0086b3;">, Q</span><span class="p">_{</span><span class="m" style="color: #099;">99</span><span class="p">}</span><span class="o" style="font-weight: 600;">)</span><span class="p">$</span> where <span class="p">$</span><span class="nb" style="color: #0086b3;">I</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i</span><span class="p">^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">l</span><span class="o" style="font-weight: 600;">)</span><span class="p">}$</span> is the <span class="p">$</span><span class="nb" style="color: #0086b3;">i</span><span class="p">$</span>th capped IPD at genomic location <span class="p">$</span><span class="nb" style="color: #0086b3;">l</span><span class="p">$</span>, <span class="p">$</span><span class="nb" style="color: #0086b3;">R</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i</span><span class="p">^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">l</span><span class="o" style="font-weight: 600;">)</span><span class="p">}$</span> is the <span class="p">$</span><span class="nb" style="color: #0086b3;">i</span><span class="p">$</span>th raw IPD and <span class="p">$</span><span class="nb" style="color: #0086b3;">Q</span><span class="p">_{</span><span class="m" style="color: #099;">99</span><span class="p">}$</span> is the <span class="p">$</span><span class="m" style="color: #099;">99</span><span class="p">$</span>th percentile IPD over all IPD observations.</span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="tex">We summarize the capped IPDs at each positions with a sample mean and standard deviation of the mean:</span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{eqnarray}</span> </span>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="tex"><span class="k" style="font-weight: 600;">\mu</span><span class="p">_</span>l <span class="p">&</span> = <span class="p">&</span> <span class="k" style="font-weight: 600;">\frac</span><span class="p">{</span>1<span class="p">}{</span>n<span class="p">_</span>l<span class="p">}</span> <span class="k" style="font-weight: 600;">\sum</span><span class="p">_</span>i R<span class="p">_</span>i<span class="p">^{</span>(l)<span class="p">}</span> <span class="k" style="font-weight: 600;">\\</span></span>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="tex"><span class="k" style="font-weight: 600;">\sigma</span><span class="p">_</span>l<span class="p">^</span>2 <span class="p">&</span> = <span class="p">&</span> <span class="k" style="font-weight: 600;">\frac</span><span class="p">{</span>1<span class="p">}{</span>n<span class="p">_</span>l<span class="p">}</span> <span class="k" style="font-weight: 600;">\sqrt</span><span class="p">{</span><span class="k" style="font-weight: 600;">\sum</span><span class="p">_</span>i (R<span class="p">_</span>i<span class="p">^{</span>(l)<span class="p">}</span> - m<span class="p">_</span>l)<span class="p">^</span>2 <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{eqnarray}</span></span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="tex"><span class="k" style="font-weight: 600;">\section</span><span class="p">{</span>Control IPDs<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="tex">Modification detection proceeds by comparing the observed mean IPD <span class="p">$</span><span class="nb" style="color: #0086b3;">m</span><span class="p">_</span><span class="nb" style="color: #0086b3;">l</span><span class="p">$</span> with the expected mean IPD for unmodified DNA at that location. In case-control mode we sequence a sample of DNA from the same organism that has been <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>whole genome amplified<span class="p">}</span> (WGA) to preserve the DNA sequence while removing all base modifications. In this mode of operation we summarize the IPDs observed in the control sample in the same way as the case sample, then proceed to the modification detection step. If a control sample is used we compute <span class="p">$</span><span class="nv" style="color: #008080;">\mu</span><span class="p">_</span><span class="nb" style="color: #0086b3;">l</span><span class="p">^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">c</span><span class="o" style="font-weight: 600;">)</span><span class="p">}$</span> and <span class="p">$</span><span class="nv" style="color: #008080;">\sigma</span><span class="p">_</span><span class="nb" style="color: #0086b3;">l</span><span class="p">^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">c</span><span class="o" style="font-weight: 600;">)</span><span class="p">}$</span> for each position on the control sample data as in Section <span class="k" style="font-weight: 600;">\ref</span><span class="p">{</span>sec:prep<span class="p">}</span>.</span>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="tex"><span class="k" style="font-weight: 600;">\subsection</span><span class="p">{</span><span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>in-silico<span class="p">}</span> Control<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="tex">An alternative to the <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>case-control<span class="p">}</span> paradigm is to construct an <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>in-silico<span class="p">}</span> model to predict the mean IPD  unmodified DNA given the local sequence context. We use the Gradient Boosting Machines <span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>gradientboost<span class="p">}</span> to construct a function <span class="p">$</span><span class="nb" style="color: #0086b3;">Q</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">c</span><span class="p">}</span><span class="o" style="font-weight: 600;">)</span><span class="p">$</span> that returns an estimate of the mean IPD given a DNA context <span class="p">$</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">c</span><span class="p">}</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\{</span><span class="nb" style="color: #0086b3;">c</span><span class="p">_{</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">8</span><span class="p">}</span><span class="nb" style="color: #0086b3;">, c</span><span class="p">_{</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">7</span><span class="p">}</span><span class="nb" style="color: #0086b3;">, ... ,c</span><span class="p">_</span><span class="m" style="color: #099;">0</span><span class="nb" style="color: #0086b3;">, c</span><span class="p">_</span><span class="m" style="color: #099;">1</span><span class="nb" style="color: #0086b3;">, .., c</span><span class="p">_</span><span class="m" style="color: #099;">3</span><span class="nv" style="color: #008080;">\}</span><span class="p">$</span> where <span class="p">$</span><span class="nb" style="color: #0086b3;">c</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i </span><span class="nv" style="color: #008080;">\in</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\{</span><span class="nb" style="color: #0086b3;">A, C, G, T</span><span class="nv" style="color: #008080;">\}</span><span class="p">$</span> encodes the DNA sequence surrounding <span class="p">$</span><span class="nb" style="color: #0086b3;">c</span><span class="p">_</span><span class="m" style="color: #099;">0</span><span class="p">$</span>. The IPD prediction <span class="p">$</span><span class="nb" style="color: #0086b3;">Q</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">c</span><span class="p">}</span><span class="o" style="font-weight: 600;">)</span><span class="p">$</span> corresponds to the IPD of base <span class="p">$</span><span class="nb" style="color: #0086b3;">c</span><span class="p">_</span><span class="m" style="color: #099;">0</span><span class="p">$</span>. Initially we generated models spanning <span class="p">$</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">15</span><span class="p">$</span> to <span class="p">$</span><span class="o" style="font-weight: 600;">+</span><span class="m" style="color: #099;">15</span><span class="p">$</span> base pairs to determine the appropriate size of the context vector. Figure <span class="k" style="font-weight: 600;">\ref</span><span class="p">{</span>fig:position-influence<span class="p">}</span> shows the GBM variable influence measure relative to the cognate base. We chose a context window of <span class="p">$</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">8</span><span class="p">$</span> to <span class="p">$</span><span class="m" style="color: #099;">3</span><span class="p">$</span> by cutting off the window when the influence becomes small.  The extent of the window agrees with the set of bases interacting with the polymerase in crystal structures.  Each base <span class="p">$</span><span class="nb" style="color: #0086b3;">c</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i</span><span class="p">$</span> in the context vector becomes a feature available to GBM learning machinery. We chose GBM because it naturally handles categorical feature variables, and it automatically discovers complicated variable interactions. We a shrinkage (or learning rate) of <span class="p">$</span><span class="nv" style="color: #008080;">\lambda</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">0</span><span class="nb" style="color: #0086b3;">.</span><span class="m" style="color: #099;">15</span><span class="p">$</span>. We fit <span class="p">$</span><span class="nb" style="color: #0086b3;">T</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">60000</span><span class="p">$</span> trees in our ensemble, each with a maximum interaction depth of <span class="p">$</span><span class="nb" style="color: #0086b3;">K</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">12</span><span class="p">$</span>  We used the <span class="k" style="font-weight: 600;">\textsf</span><span class="p">{</span>gbm<span class="p">}</span> package<span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>gbm<span class="p">}</span> from R for initial experiments, and a custom port of the code for production training.  The <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>in-silico<span class="p">}</span> IPD model <span class="p">$</span><span class="nb" style="color: #0086b3;">Q</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">c</span><span class="p">}</span><span class="o" style="font-weight: 600;">)</span><span class="p">$</span> will have some bias compared to the true mean at some genomic location due to noise in the training dataset that was not generalized out in the training procedure, in or due to the residual influence of sequence outside of the context window. </span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{eqnarray}</span></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="tex"><span class="k" style="font-weight: 600;">\mu</span><span class="p">_</span>l<span class="p">^{</span>(c)<span class="p">}</span> <span class="p">&</span> = <span class="p">&</span> Q(<span class="k" style="font-weight: 600;">\mathbf</span><span class="p">{</span>Ctx<span class="p">}</span>(l)) <span class="k" style="font-weight: 600;">\\</span></span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="tex"><span class="k" style="font-weight: 600;">\sigma</span><span class="p">_</span>l<span class="p">^{</span>(c)<span class="p">}</span> <span class="p">&</span> = <span class="p">&</span> f(<span class="k" style="font-weight: 600;">\mu</span><span class="p">_</span>l<span class="p">^{</span>(c)<span class="p">}</span>)</span>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{eqnarray}</span></span>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{figure}</span></span>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{center}</span><span class="k" style="font-weight: 600;">\includegraphics</span><span class="na" style="color: #008080;">[width=5in]</span><span class="p">{</span>position-influence.png<span class="p">}</span><span class="nt" style="color: #000080;">\end{center}</span></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="tex"><span class="k" style="font-weight: 600;">\caption</span><span class="p">{</span> Influence of Base in Context Window <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="tex"><span class="k" style="font-weight: 600;">\label</span><span class="p">{</span>fig:position-influence<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{figure}</span></span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="tex"><span class="k" style="font-weight: 600;">\section</span><span class="p">{</span>Modification Detection<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="tex">We pose the modification detection problem as the detection of genome locations whose mean IPD differs significantly from the control mean. We use a Welch's <span class="p">$</span><span class="nb" style="color: #0086b3;">t</span><span class="p">$</span>-test to test for differences in the means between the case sample and the control, derived from either a control sample or the <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>in-silico<span class="p">}</span> model above.</span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="tex">The <span class="p">$</span><span class="nb" style="color: #0086b3;">t</span><span class="p">$</span>-statistic is defined as:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{eqnarray}</span></span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="tex">s<span class="p">_</span>l <span class="p">&</span> = <span class="p">&</span> = <span class="k" style="font-weight: 600;">\sqrt</span><span class="p">{</span> <span class="k" style="font-weight: 600;">\sigma</span><span class="p">_</span>l<span class="p">^</span>2 + <span class="k" style="font-weight: 600;">\sigma</span><span class="p">_</span>l<span class="p">^{</span>(c)2<span class="p">}}</span> <span class="k" style="font-weight: 600;">\\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="tex">T<span class="p">_</span>l <span class="p">&</span> = <span class="p">&</span><span class="k" style="font-weight: 600;">\frac</span><span class="p">{</span><span class="k" style="font-weight: 600;">\mu</span><span class="p">_</span>l - <span class="k" style="font-weight: 600;">\mu</span><span class="p">_</span>l<span class="p">^{</span>(c)<span class="p">}}{</span>s<span class="p">_</span>l<span class="p">}</span> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{eqnarray}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="tex">and we compute the p-value of <span class="p">$</span><span class="nb" style="color: #0086b3;">T</span><span class="p">_</span><span class="nb" style="color: #0086b3;">l</span><span class="p">$</span> under the <span class="p">$</span><span class="nb" style="color: #0086b3;">t</span><span class="p">$</span>-distribution, and report a Phred-transformed QV as well:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{eqnarray}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="tex">p <span class="p">&</span> = <span class="p">&</span> <span class="k" style="font-weight: 600;">\Pr</span>(t > T<span class="p">_</span>l) <span class="k" style="font-weight: 600;">\\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="tex"><span class="k" style="font-weight: 600;">\mathrm</span><span class="p">{</span>QV<span class="p">}</span> <span class="p">&</span> = <span class="p">&</span> -10 <span class="k" style="font-weight: 600;">\log</span><span class="p">_{</span>10<span class="p">}</span> p</span>

</pre>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{eqnarray}</span></span>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="tex"><span class="k" style="font-weight: 600;">\section</span><span class="p">{</span> Modification Identification <span class="p">}</span> </span>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="tex"><span class="k" style="font-weight: 600;">\subsection</span> <span class="p">{</span> Positive Control Model <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="tex">We extend the <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>in-silico<span class="p">}</span> model from an alphabet over DNA bases <span class="p">$</span><span class="nb" style="color: #0086b3;">c</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i </span><span class="nv" style="color: #008080;">\in</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\{</span><span class="nb" style="color: #0086b3;">A,C,G,T</span><span class="nv" style="color: #008080;">\}</span><span class="p">$</span> to an alphabet that includes the <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>modified<span class="p">}</span> bases we aim to identify: <span class="p">$</span><span class="nb" style="color: #0086b3;">c</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i </span><span class="nv" style="color: #008080;">\in</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\{</span><span class="nb" style="color: #0086b3;">A,C,G,T, </span><span class="p">^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">6</span><span class="p">}</span><span class="nb" style="color: #0086b3;">A, </span><span class="p">^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">5</span><span class="p">}</span><span class="nb" style="color: #0086b3;">C, </span><span class="p">^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">4</span><span class="p">}</span><span class="nb" style="color: #0086b3;">C </span><span class="nv" style="color: #008080;">\}</span><span class="p">$</span>. To train this model we require labeled examples of the modified bases in a reasonable diversity of background contexts.  Base modifications appearing in bacterial restriction-modification systems provide an excellent source of training data that is fairly straightforward to label. A typical bacteria will express several (generally between 2 and 7, going as high as 20) methyltranserases that specifically methylate a particular sequence context in the host genome. The expression of the methyltransferase is generally paired with the expression of a restriction enzyme whose recognition site matches that of the methyltransferase. These <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>active<span class="p">}</span> RM systems must methylate the genome nearly completely to prevent cutting of the host genome. Occasionally bacteria will carry an <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>orphan<span class="p">}</span> methyltransferase that is not paired with a restriction enzyme, which often leads to weaker  activity for that methyltransferase. We identify the <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>active<span class="p">}</span> and <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>orphan<span class="p">}</span> methyltransferases via a manual curation and use genomic positions modified by <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>active<span class="p">}</span> RM systems in our training set. For example, the common 'GATC' motif, which carries an <span class="p">$^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">6</span><span class="p">}$</span>A modification on the A will lead to training context of the form <span class="p">$</span><span class="nb" style="color: #0086b3;">c </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> </span><span class="p">{</span><span class="nb" style="color: #0086b3;"> ..., c</span><span class="p">_{</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">}</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> G, c</span><span class="p">_</span><span class="m" style="color: #099;">0</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> </span><span class="p">^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">6</span><span class="p">}</span><span class="nb" style="color: #0086b3;">A, c</span><span class="p">_</span><span class="m" style="color: #099;">1</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> T, c</span><span class="p">_</span><span class="m" style="color: #099;">2</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> T, c</span><span class="p">_</span><span class="m" style="color: #099;">3</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> C </span><span class="p">}$</span>.</span>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="tex">Our positive control training set incorporates data from 11 bacteria, with the following number of unique methylated motifs for each modification type -- <span class="k" style="font-weight: 600;">\mA</span>:36, <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>4<span class="p">}</span>:7, <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>5<span class="p">}</span>:7.</span>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="tex"><span class="k" style="font-weight: 600;">\subsection</span><span class="p">{</span>Viterbi Decoding<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="tex">Let <span class="p">$</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">S</span><span class="p">}</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> s</span><span class="p">_</span><span class="m" style="color: #099;">1</span><span class="nb" style="color: #0086b3;">, s</span><span class="p">_</span><span class="m" style="color: #099;">2</span><span class="nb" style="color: #0086b3;">, s</span><span class="p">_</span><span class="m" style="color: #099;">3</span><span class="nb" style="color: #0086b3;">, ... s</span><span class="p">_</span><span class="nb" style="color: #0086b3;">n</span><span class="p">$</span> be the unmodified DNA sequence (<span class="p">$</span><span class="nb" style="color: #0086b3;">s</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i </span><span class="nv" style="color: #008080;">\in</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\{</span><span class="nb" style="color: #0086b3;">A,C,G,T</span><span class="nv" style="color: #008080;">\}</span><span class="p">$</span>). Let <span class="p">$</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> m</span><span class="p">_</span><span class="m" style="color: #099;">1</span><span class="nb" style="color: #0086b3;">, m</span><span class="p">_</span><span class="m" style="color: #099;">2</span><span class="nb" style="color: #0086b3;">, m</span><span class="p">_</span><span class="m" style="color: #099;">3</span><span class="nb" style="color: #0086b3;">, ..., m</span><span class="p">_</span><span class="nb" style="color: #0086b3;">n</span><span class="p">$</span> be a DNA sequence carrying modifications (<span class="p">$</span><span class="nb" style="color: #0086b3;">m</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i </span><span class="nv" style="color: #008080;">\in</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\{</span><span class="nb" style="color: #0086b3;">A,C,G,T, </span><span class="p">^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">6</span><span class="p">}</span><span class="nb" style="color: #0086b3;">A, </span><span class="p">^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">5</span><span class="p">}</span><span class="nb" style="color: #0086b3;">C, </span><span class="p">^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">4</span><span class="p">}</span><span class="nb" style="color: #0086b3;">C </span><span class="nv" style="color: #008080;">\}</span><span class="p">$</span>). A modification removal <span class="p">$</span><span class="nb" style="color: #0086b3;">R</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">m</span><span class="o" style="font-weight: 600;">)</span><span class="p">$</span> operation maps a modification to it's unmodified base - so <span class="p">$</span><span class="nb" style="color: #0086b3;">R</span><span class="o" style="font-weight: 600;">(</span><span class="p">^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">6</span><span class="p">}</span><span class="nb" style="color: #0086b3;">A</span><span class="o" style="font-weight: 600;">)</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> A, R</span><span class="o" style="font-weight: 600;">(</span><span class="p">^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">5</span><span class="p">}</span><span class="nb" style="color: #0086b3;">C</span><span class="o" style="font-weight: 600;">)</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> C, R</span><span class="o" style="font-weight: 600;">(</span><span class="p">^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">4</span><span class="p">}</span><span class="nb" style="color: #0086b3;">C</span><span class="o" style="font-weight: 600;">)</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> C</span><span class="p">$</span>.  The modified sequence <span class="p">$</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}$</span> is constrained to maintain the base identity of the sequence: <span class="p">$</span><span class="nb" style="color: #0086b3;">R</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">m</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i</span><span class="o" style="font-weight: 600;">)</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> s</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i</span><span class="p">$</span>.  We can model the likelihood of each observed IPD data point along the sequence <span class="p">$</span><span class="nv" style="color: #008080;">\mu</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i</span><span class="p">$</span> in the same manner: </span>

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="tex"><span class="p">$$</span></span>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="tex"><span class="nv" style="color: #008080;">\log</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\Pr</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">O</span><span class="p">}</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\mid</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}</span><span class="o" style="font-weight: 600;">)</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\sum</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i </span><span class="nv" style="color: #008080;">\log</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\Pr</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">O</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i </span><span class="nv" style="color: #008080;">\mid</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\mathcal</span><span class="p">{</span><span class="nb" style="color: #0086b3;">C</span><span class="p">}</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}</span><span class="nb" style="color: #0086b3;">, i</span><span class="o" style="font-weight: 600;">))</span></span>

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="tex"><span class="p">$$</span></span>

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="tex">where <span class="p">$</span><span class="nv" style="color: #008080;">\mathcal</span><span class="p">{</span><span class="nb" style="color: #0086b3;">C</span><span class="p">}</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}</span><span class="nb" style="color: #0086b3;">, i</span><span class="o" style="font-weight: 600;">)</span><span class="p">$</span> is the <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>context<span class="p">}</span> function that snips out the -8 to +3 bp context from sequence <span class="p">$</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}$</span> around position <span class="p">$</span><span class="nb" style="color: #0086b3;">i</span><span class="p">$</span>.</span>

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="tex">IPD observations <span class="p">$</span><span class="nb" style="color: #0086b3;">O</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i</span><span class="p">$</span> are assumed independent given the context <span class="p">$</span><span class="nv" style="color: #008080;">\mathcal</span><span class="p">{</span><span class="nb" style="color: #0086b3;">C</span><span class="p">}</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}</span><span class="nb" style="color: #0086b3;">, i</span><span class="o" style="font-weight: 600;">)</span><span class="p">$</span>.  We seek to find the modification sequence <span class="p">$</span><span class="nv" style="color: #008080;">\hat</span><span class="p">{</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}}$</span> that maximizes the likelihood of IPD observations: </span>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="tex"><span class="p">$$</span></span>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="tex"><span class="nv" style="color: #008080;">\hat</span><span class="p">{</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}}</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\argmax</span><span class="p">_{</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}}</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\sum</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i </span><span class="nv" style="color: #008080;">\log</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\Pr</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">O</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i </span><span class="nv" style="color: #008080;">\mid</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\mathcal</span><span class="p">{</span><span class="nb" style="color: #0086b3;">C</span><span class="p">}</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}</span><span class="nb" style="color: #0086b3;">, i</span><span class="o" style="font-weight: 600;">))</span><span class="nb" style="color: #0086b3;"> </span></span>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="tex"><span class="p">$$</span></span>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="tex">Again we use the t-distribution to model the likelihood of the observed IPDs, given a mean prediction generated by the <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>in-silico<span class="p">}</span> IPD model:</span>

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{eqnarray}</span></span>

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="tex">T<span class="p">_</span>i <span class="p">&</span> = <span class="p">&</span> <span class="k" style="font-weight: 600;">\frac</span><span class="p">{</span><span class="k" style="font-weight: 600;">\mu</span><span class="p">_</span>i - Q(<span class="k" style="font-weight: 600;">\mathcal</span><span class="p">{</span>C<span class="p">}</span>(<span class="k" style="font-weight: 600;">\mathbf</span><span class="p">{</span>M<span class="p">}</span>, i)<span class="p">}{</span>s<span class="p">_</span>i<span class="p">}</span> <span class="k" style="font-weight: 600;">\\</span></span>

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="tex">Pr(O<span class="p">_</span>i <span class="k" style="font-weight: 600;">\mid</span> <span class="k" style="font-weight: 600;">\mathcal</span><span class="p">{</span>C<span class="p">}</span>(<span class="k" style="font-weight: 600;">\mathbf</span><span class="p">{</span>M<span class="p">}</span>, i)) <span class="p">&</span> = <span class="p">&</span> f(T<span class="p">_</span>i)</span>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{eqnarray}</span></span>

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<pre style="margin: 0;">-<span id="LC116" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="tex">where <span class="p">$</span><span class="nb" style="color: #0086b3;">f</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">T</span><span class="o" style="font-weight: 600;">)</span><span class="p">$</span> is the <span class="p">$</span><span class="nb" style="color: #0086b3;">t</span><span class="p">$</span>-distribution PDF.</span>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="tex">We find the maximum-likelihood modification sequence by applying the Viterbi algorithm<span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>forney1973viterbi<span class="p">}</span>. At each position <span class="p">$</span><span class="nb" style="color: #0086b3;">i</span><span class="p">$</span> we define <span class="p">$</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">H</span><span class="p">}^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">i</span><span class="o" style="font-weight: 600;">)</span><span class="p">}$</span>, the set of all possible modification contexts centered at <span class="p">$</span><span class="nb" style="color: #0086b3;">i</span><span class="p">$</span> with a unmodified sequence that matches the reference sequence. In order to reduce the algorithm run time, we reduce the size of <span class="p">$</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">H</span><span class="p">}^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">i</span><span class="o" style="font-weight: 600;">)</span><span class="p">}$</span> by only considering alternatives that have some supporting evidence in the nearby single-site <span class="p">$</span><span class="nb" style="color: #0086b3;">p</span><span class="p">$</span>-values. Here we show the general formulation:</span>

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="tex"><span class="p">$$</span></span>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="tex"><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">H</span><span class="p">}^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">i</span><span class="o" style="font-weight: 600;">)</span><span class="p">}</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\{</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\mathcal</span><span class="p">{</span><span class="nb" style="color: #0086b3;">C</span><span class="p">}</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}</span><span class="nb" style="color: #0086b3;">, i</span><span class="o" style="font-weight: 600;">)</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\mid</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}</span><span class="nb" style="color: #0086b3;">, R</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">m</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i</span><span class="o" style="font-weight: 600;">)</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> s</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i </span><span class="nv" style="color: #008080;">\}</span><span class="nb" style="color: #0086b3;"> </span></span>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="tex"><span class="p">$$</span></span>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="tex">The Viterbi forward matrix <span class="p">$</span><span class="nv" style="color: #008080;">\alpha</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">H</span><span class="p">^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">i</span><span class="o" style="font-weight: 600;">)</span><span class="p">}_</span><span class="nb" style="color: #0086b3;">j, i</span><span class="o" style="font-weight: 600;">)</span><span class="p">$</span> is defined recursively: The first argument is the current state <span class="p">$</span><span class="nb" style="color: #0086b3;">H</span><span class="p">^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">i</span><span class="o" style="font-weight: 600;">)</span><span class="p">}_</span><span class="nb" style="color: #0086b3;">j</span><span class="p">$</span> drawn from the possible modification configurations <span class="p">$</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">H</span><span class="p">}^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">i</span><span class="o" style="font-weight: 600;">)</span><span class="p">}$</span>; the second argument is the position <span class="p">$</span><span class="nb" style="color: #0086b3;">i</span><span class="p">$</span>.</span>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="tex"><span class="p">$$</span></span>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="tex"><span class="nv" style="color: #008080;">\alpha</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">H</span><span class="p">^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">i</span><span class="o" style="font-weight: 600;">)</span><span class="p">}_</span><span class="nb" style="color: #0086b3;">j, i</span><span class="o" style="font-weight: 600;">)</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\max</span><span class="p">_{</span><span class="nb" style="color: #0086b3;">K </span><span class="nv" style="color: #008080;">\in</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">H</span><span class="p">}^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">i</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span><span class="p">}}</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\alpha</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">K, i</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\Pr</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">O</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i </span><span class="nv" style="color: #008080;">\mid</span><span class="nb" style="color: #0086b3;"> H</span><span class="p">^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">i</span><span class="o" style="font-weight: 600;">)</span><span class="p">}_</span><span class="nb" style="color: #0086b3;">j</span><span class="o" style="font-weight: 600;">)</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\;</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">SM</span><span class="p">}</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">K, H</span><span class="p">^{</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">i</span><span class="o" style="font-weight: 600;">)</span><span class="p">}_</span><span class="nb" style="color: #0086b3;">j</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="tex"><span class="p">$$</span></span>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="tex"><span class="p">$</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">SM</span><span class="p">}</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">K, L</span><span class="o" style="font-weight: 600;">)</span><span class="nb" style="color: #0086b3;"> </span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="m" style="color: #099;">1</span><span class="p">}</span><span class="nv" style="color: #008080;">\{</span><span class="nb" style="color: #0086b3;">K</span><span class="p">_</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">L</span><span class="p">_</span><span class="m" style="color: #099;">2</span><span class="nb" style="color: #0086b3;">, ..., K</span><span class="p">_{</span><span class="m" style="color: #099;">11</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">L</span><span class="p">_{</span><span class="m" style="color: #099;">12</span><span class="p">}</span><span class="nv" style="color: #008080;">\}</span><span class="p">$</span> is the <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>context matching function<span class="p">}</span>, where <span class="p">$</span><span class="nb" style="color: #0086b3;">K</span><span class="p">$</span> and <span class="p">$</span><span class="nb" style="color: #0086b3;">L</span><span class="p">$</span> are 12 base context strings. It returns <span class="p">$</span><span class="m" style="color: #099;">1</span><span class="p">$</span> if the last 11 bases of <span class="p">$</span><span class="nb" style="color: #0086b3;">K</span><span class="p">$</span> match the first 11 bases of <span class="p">$</span><span class="nb" style="color: #0086b3;">L</span><span class="p">$</span>, and <span class="p">$</span><span class="m" style="color: #099;">0</span><span class="p">$</span> otherwise. This enforces the constraint that modification sequence contexts are self-consistent for all paths through the Viterbi matrix.</span>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="tex">The standard Viterbi traceback procedure yields the maximum-likelihood modification state at each genomic position. We compute a Modification QV for each modification in the ML configuration by comparing the likelihood of the best modification sequence to the likelihood with a given modification set back to the canonical base:</span>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{eqnarray}</span></span>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="tex">p<span class="p">_</span>i <span class="p">&</span> = <span class="p">&</span> <span class="k" style="font-weight: 600;">\frac</span><span class="p">{</span><span class="k" style="font-weight: 600;">\Pr</span>(<span class="k" style="font-weight: 600;">\mathbf</span><span class="p">{</span>O<span class="p">}</span> <span class="k" style="font-weight: 600;">\mid</span> R(<span class="k" style="font-weight: 600;">\hat</span><span class="p">{</span><span class="k" style="font-weight: 600;">\mathbf</span><span class="p">{</span>M<span class="p">}}</span>, i))<span class="p">}</span> <span class="p">{</span><span class="k" style="font-weight: 600;">\log</span> <span class="k" style="font-weight: 600;">\Pr</span>(<span class="k" style="font-weight: 600;">\mathbf</span><span class="p">{</span>O<span class="p">}</span> <span class="k" style="font-weight: 600;">\mid</span> R(<span class="k" style="font-weight: 600;">\hat</span><span class="p">{</span><span class="k" style="font-weight: 600;">\mathbf</span><span class="p">{</span>M<span class="p">}}</span>, i)) + <span class="k" style="font-weight: 600;">\log</span> <span class="k" style="font-weight: 600;">\Pr</span>(<span class="k" style="font-weight: 600;">\mathbf</span><span class="p">{</span>O<span class="p">}</span> <span class="k" style="font-weight: 600;">\mid</span> <span class="k" style="font-weight: 600;">\mathbf</span><span class="p">{</span>M<span class="p">}</span>') <span class="p">}</span> <span class="k" style="font-weight: 600;">\\</span></span>

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="tex"><span class="k" style="font-weight: 600;">\mathrm</span><span class="p">{</span>QV<span class="p">}_</span>i <span class="p">&</span> = <span class="p">&</span> -10 <span class="k" style="font-weight: 600;">\log</span><span class="p">_{</span>10<span class="p">}</span> p<span class="p">_</span>e</span>

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{eqnarray}</span></span>

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="tex">where <span class="p">$</span><span class="nb" style="color: #0086b3;">R</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">\hat</span><span class="p">{</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}}</span><span class="nb" style="color: #0086b3;">, i</span><span class="o" style="font-weight: 600;">))</span><span class="p">$</span> denotes the <span class="p">$</span><span class="nv" style="color: #008080;">\hat</span><span class="p">{</span><span class="nv" style="color: #008080;">\mathbf</span><span class="p">{</span><span class="nb" style="color: #0086b3;">M</span><span class="p">}}$</span> with base <span class="p">$</span><span class="nb" style="color: #0086b3;">m</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i</span><span class="p">$</span> converted to the unmodified base <span class="p">$</span><span class="nb" style="color: #0086b3;">R</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">m</span><span class="p">_</span><span class="nb" style="color: #0086b3;">i</span><span class="o" style="font-weight: 600;">)</span><span class="p">$</span>.</span>

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="tex"><span class="k" style="font-weight: 600;">\section</span><span class="p">{</span>Results<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="tex"><span class="k" style="font-weight: 600;">\subsection</span><span class="p">{</span>Detection Performance<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="tex">Figure <span class="k" style="font-weight: 600;">\ref</span><span class="p">{</span>fig:ecoli-roc<span class="p">}</span> shows the ROC curve for single-site detection of <span class="p">$^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">6</span><span class="p">}$</span>A in <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>E.coli<span class="p">}</span>, for data from varying numbers of SMRT Cells. In these data we get the following coverage levels: 2 cells: 32x per strand, 4 cells: 65x per strand, 6 cells: 95x per strand. The <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>E.coli<span class="p">}</span> strain tested here has three methylated motifs: G<span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>A<span class="p">}</span>TC, GC<span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>A<span class="p">}</span>CNNNNNNGTT, A<span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>A<span class="p">}</span>CNNNNNNGTGC, with a total of 39430 sites matching one of those motifs.   Commonly, we observe a handful of sites that match a methylated motif without any detected methylation. Generally both strands of paired motif will be unmethylated.  We don't account for this effect, causing the true positive rate to saturate below 100<span class="k" style="font-weight: 600;">\%</span>.</span>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{figure}</span></span>

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{center}</span><span class="k" style="font-weight: 600;">\includegraphics</span><span class="na" style="color: #008080;">[width=5in]</span><span class="p">{</span>ecoli-roc.png<span class="p">}</span><span class="nt" style="color: #000080;">\end{center}</span></span>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="tex"><span class="k" style="font-weight: 600;">\caption</span><span class="p">{</span> ROC for <span class="p">$^</span><span class="nv" style="color: #008080;">\textrm</span><span class="p">{</span><span class="nb" style="color: #0086b3;">m</span><span class="m" style="color: #099;">6</span><span class="p">}$</span>A detection in <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>E.coli<span class="p">}</span> genome <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="tex"><span class="k" style="font-weight: 600;">\label</span><span class="p">{</span>fig:ecoli-roc<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{figure}</span></span>

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="tex"><span class="k" style="font-weight: 600;">\subsection</span><span class="p">{</span>Identification Performance<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="tex">We tested the modification identification capability on the bacteria <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>Desulfurobacterium thermolithotrophum<span class="p">}</span>, which carries RM systems using <span class="k" style="font-weight: 600;">\mA</span>, <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>5<span class="p">}</span>, and <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>4<span class="p">}</span> modifications. The motif CA<span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>C<span class="p">}</span>C is modified with <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>4<span class="p">}</span>, GG<span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>C<span class="p">}</span>C with <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>5<span class="p">}</span>, and G<span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>A<span class="p">}</span>TC with <span class="k" style="font-weight: 600;">\mA</span>. Table <span class="k" style="font-weight: 600;">\ref</span><span class="p">{</span>table-confusion<span class="p">}</span> shows that we can accurately separate <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>4<span class="p">}</span> and <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>5<span class="p">}</span> modifications, while accurately calling <span class="k" style="font-weight: 600;">\mA</span>. The TET treatment protocol that amplifies the <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>5<span class="p">}</span> signal appears to negatively impact the strength of the <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>4<span class="p">}</span> signal.  Work is in progress to mitigate this effect during the sample preparation.</span>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{table}</span></span>

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="tex"><span class="k" style="font-weight: 600;">\centering</span></span>

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{tabular}</span><span class="p">{</span>c c c c c c<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="tex">Motif <span class="p">&</span> Not Detected <span class="p">&</span> <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>4<span class="p">}</span> <span class="p">&</span> <span class="k" style="font-weight: 600;">\mC</span><span class="p">{</span>5<span class="p">}</span> <span class="p">&</span> <span class="k" style="font-weight: 600;">\mA</span> <span class="p">&</span> modified<span class="k" style="font-weight: 600;">\_</span>base <span class="k" style="font-weight: 600;">\\</span></span>

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="tex"><span class="k" style="font-weight: 600;">\hline</span> </span>

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="tex">CACC <span class="p">&</span>   3830 <span class="p">&</span>  <span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>1222<span class="p">}</span> <span class="p">&</span>    10 <span class="p">&</span>    0  <span class="p">&</span>      114 <span class="k" style="font-weight: 600;">\\</span></span>

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="tex">GGCC <span class="p">&</span>    235 <span class="p">&</span>    0 <span class="p">&</span> <span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>1065<span class="p">}</span> <span class="p">&</span>    0  <span class="p">&</span>       4  <span class="k" style="font-weight: 600;">\\</span></span>

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="tex">GATC <span class="p">&</span>    66 <span class="p">&</span>    0 <span class="p">&</span>    0 <span class="p">&</span> <span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>4836<span class="p">}</span>  <span class="p">&</span>       0 <span class="k" style="font-weight: 600;">\\</span></span>

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="tex">None <span class="p">&</span>     <span class="p">&</span>   85 <span class="p">&</span>   98 <span class="p">&</span>   93  <span class="p">&</span>       21799  <span class="k" style="font-weight: 600;">\\</span></span>

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{tabular}</span></span>

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="tex"><span class="k" style="font-weight: 600;">\caption</span><span class="p">{</span>Modification Identification Confusion Matrix<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="tex"><span class="k" style="font-weight: 600;">\label</span><span class="p">{</span>table-confusion<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{table}</span></span>

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="tex"><span class="k" style="font-weight: 600;">\bibdata</span><span class="p">{</span>kinetics<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="tex"><span class="k" style="font-weight: 600;">\bibliography</span><span class="p">{</span>kinetics<span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="tex"><span class="k" style="font-weight: 600;">\bibliographystyle</span><span class="p">{</span>unsrt<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="tex"><span class="k" style="font-weight: 600;">\vspace</span><span class="p">{</span>1in<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="tex"><span class="k" style="font-weight: 600;">\small</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC178" class="line" lang="tex">For Research Use Only. Not for use in diagnostic procedures. © Copyright 2012, Pacific Biosciences of California, Inc. All rights reserved. Information in this document is subject to change without notice. Pacific Biosciences assumes no responsibility for any errors or omissions in this document. Certain notices, terms, conditions and/or use restrictions may pertain to your use of Pacific Biosciences products and/or third party products. Please refer to the applicable Pacific Biosciences Terms and Conditions of Sale and to the applicable license terms at <span class="k" style="font-weight: 600;">\url</span><span class="p">{</span>http://www.pacificbiosciences.com/licenses.html<span class="p">}</span>.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC179" class="line" lang="tex">Pacific Biosciences, the Pacific Biosciences logo, PacBio, SMRT and SMRTbell are trademarks of Pacific Biosciences in the United States and/or certain other countries. All other trademarks are the sole property of their respective owners.  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC180" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC181" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{document}</span> </span></pre>

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