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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/poretools">Debian Med / poretools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/poretools/commit/985833f1a2e000e3d47a470f6c4a04a480f6f847">985833f1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-15T21:39:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Apply patch by Steve Langasek <steve.langasek@canonical.com>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/poretools/commit/2f3f1e9ac89e6f0798f5818571d19efebedd8e5b">2f3f1e9a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-15T21:41:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Close bug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/poretools/commit/1a7d876503977130e855417d43ed8aed191abd83">1a7d8765</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-15T21:43:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add myself to Uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/poretools/commit/0ef295c46713331dee650df3c65fbe95e5d50511">0ef295c4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-15T21:43:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/poretools/commit/a33ec836de9f96ca77be5144733b1b97898d5dce">a33ec836</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-15T21:44:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/poretools/commit/6c4e3ef3cafa2d44949f49957c82625f88b8b3a8">6c4e3ef3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-15T21:44:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Secure URI in copyright format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/poretools/commit/4a8b8ed1ed6b9eceed279125032794db39f80bab">4a8b8ed1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-15T21:44:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use secure URI in Homepage field.
Fixes lintian: homepage-field-uses-insecure-uri
See https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/poretools/commit/c025b834827190f6bee251ba994a7288134486a6">c025b834</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-15T21:56:46Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
<span class="new-file">
+
debian/patches/python3.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
</span>
</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/poretools/compare/9f6d6dc9b18c2a3db6573f1f8245bc450dd352cc...c025b834827190f6bee251ba994a7288134486a6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">poretools (0.6.0+dfsg-4) unstable; urgency=medium</span>
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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 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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Steve Langasek ]</span>
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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Port to Python3</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #934845</span>
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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"></span>
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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">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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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"> * Afif removed himself from Uploaders</span>
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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"> * Add myself to Uploaders</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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"> * Standards-Version: 4.4.0</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Secure URI in copyright format</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> * Use secure URI in Homepage field.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 15 Aug 2019 23:44:33 +0200</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">poretools (0.6.0+dfsg-3) unstable; urgency=low</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/poretools/compare/9f6d6dc9b18c2a3db6573f1f8245bc450dd352cc...c025b834827190f6bee251ba994a7288134486a6#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<a href="https://salsa.debian.org/med-team/poretools/compare/9f6d6dc9b18c2a3db6573f1f8245bc450dd352cc...c025b834827190f6bee251ba994a7288134486a6#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: poretools</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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3
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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4
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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6
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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7
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> python-all,</span>
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8
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> python-setuptools,</span>
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9
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python<span class="idiff left right">-h5py (>= 2.2)</span>,</span>
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10
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> python-matplotlib,</span>
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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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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> python-seaborn,</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> python-pandas</span>
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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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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.5</span></span>
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<td class="diff-line-num new old_line" data-linenumber="14" 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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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-all,</span>
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<td class="diff-line-num new old_line" data-linenumber="14" 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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-setuptools,</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python<span class="idiff left right">3-h5py</span>,</span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-matplotlib,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-seaborn,</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-pandas</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.0</span></span>
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14
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/poretools</span>
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15
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/poretools.git</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Homepage: http://poretools.readthedocs.org</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Homepage: http<span class="idiff left right">s</span>://poretools.readthedocs.org</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Package: poretools</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> ${python:Depends},</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> python-pkg-resources</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> ${python<span class="idiff left right">3</span>:Depends},</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-pkg-resources</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Description: toolkit for nanopore nucleotide sequencing data</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> poretools is a flexible toolkit for exploring datasets generated by nanopore</span>
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25
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> sequencing devices from MinION for the purposes of quality control and</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/poretools/compare/9f6d6dc9b18c2a3db6573f1f8245bc450dd352cc...c025b834827190f6bee251ba994a7288134486a6#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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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: poretools</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Upstream-Contact: Aaron Quinlan <arq5x@virginia.edu></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Source: https://github.com/arq5x/poretools</span>
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<li id="e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
<a href="https://salsa.debian.org/med-team/poretools/compare/9f6d6dc9b18c2a3db6573f1f8245bc450dd352cc...c025b834827190f6bee251ba994a7288134486a6#e246f69e945a7c2e9a8e25cfacfcac7714c92b69"><strong>debian/patches/python3.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: port to python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Python2 is obsolete. Port this code to python3.</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> Changes consist of 2to3 output, plus fixes for tab vs. space issues, and</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> a fix to argparse handling when we're called with no arguments.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Author: Steve Langasek <steve.langasek@ubuntu.com></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Last-Modified: 2019-08-15</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/934845</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">Index: poretools-0.6.0+dfsg/setup.py</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> version_py = os.path.join(os.path.dirname(__file__), 'poretools', 'version.py')</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> version = open(version_py).read().strip().split('=')[-1].replace('"','').strip()</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print version</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print(version)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> long_description = """</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> ``poretools`` is a toolset for working with nanopore sequencing data'</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import scripts</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from Fast5File import *</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from version import __version__</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import scripts</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .Fast5File import *</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .version import __version__</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/Fast5File.py</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/Fast5File.py</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/Fast5File.py</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -11,8 +11,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> # poretools imports</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import formats</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from Event import Event</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import formats</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .Event import Event</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> fastq_paths = {</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> 'closed' : {},</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="p">@@ -63,7 +63,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> def __iter__(self):</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> return self</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def next(self):</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def __next__(self):</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> if len(self.files) > 0:</span>
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<td class="diff-line-num new new_line" data-linenumber="57" 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">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> return self.files.pop(0)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -93,9 +93,9 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="60" 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">
60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> def __iter__(self):</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> return self</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def next(self):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="64" 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">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def __next__(self):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="65" 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">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> try:</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return Fast5File(self.files.next(), self.group)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="67" 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">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return Fast5File(next(self.files), self.group)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> except Exception as e:</span>
</pre>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> # cleanup our mess</span>
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<td class="diff-line-num new new_line" data-linenumber="70" 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">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> if self.set_type == FAST5SET_TARBALL:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="71" 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">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="p">@@ -156,9 +156,9 @@</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="72" 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">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> def __iter__(self):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> return self</span>
</pre>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def next(self):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def __next__(self):</span></span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> while True:</span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tarinfo = self._tarfile.next()</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tarinfo = next(self._tarfile)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> if tarinfo is None:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> raise StopIteration</span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> elif self._fast5_filename_filter(tarinfo.name):</span>
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="p">@@ -211,7 +211,7 @@</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> try:</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> self.hdf5file = h5py.File(self.filename, 'r')</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> return True</span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Exception, e:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="88" 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">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Exception as e:</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> logger.warning("Cannot open file: %s. Perhaps it is corrupt? Moving on.\n" % self.filename)</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> return False</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> </span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="p">@@ -327,7 +327,7 @@</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> self._extract_fastas_from_fast5()</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> self.have_fastas = True</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> </span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return self.fastas</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return self.fastas</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> </span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> def get_fastq(self):</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> """</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="p">@@ -465,7 +465,7 @@</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> https://github.com/arq5x/poretools/issues""" % (self.filename, reason)</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> sys.exit(msg)</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> </span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def find_read_number_block_fixed_raw(self):</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def find_read_number_block_fixed_raw(self):</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> New-style FAST5/HDF5 structure:</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> There is a fixed 'Raw/Reads' node with only one 'read_NNN' item</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="p">@@ -477,7 +477,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> if raw_reads is None:</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> return None</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- reads = raw_reads.keys()</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ reads = list(raw_reads.keys())</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> if len(reads)==0:</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> self.hdf_internal_error("Raw/Reads group does not contain any items")</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> if len(reads)>1:</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="p">@@ -489,7 +489,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> self.hdf_internal_error("Failed to get HDF5 item '%s'"% (path))</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> return node</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def find_read_number_block(self):</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def find_read_number_block(self):</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> """Returns the node of the 'Read_NNN' information, or None if not</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> found"""</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> node = self.find_read_number_block_link()</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="p">@@ -652,31 +652,31 @@</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> self._get_metadata()</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> self.have_metadata = True</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def get_host_name(self):</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """</span></span>
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<td class="diff-line-num new new_line" data-linenumber="134" 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">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Return the MinKNOW host computer name.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if self.have_metadata is False:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._get_metadata()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="138" 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">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.have_metadata = True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" 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">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- try:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return self.keyinfo['tracking_id'].attrs['hostname']</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" 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">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return None</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if self.have_metadata is False:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" 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">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._get_metadata()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" 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">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.have_metadata = True</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def get_host_name(self):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ """</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Return the MinKNOW host computer name.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ """</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if self.have_metadata is False:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="153" 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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self._get_metadata()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.have_metadata = True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="155" 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">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return self.keyinfo['tracking_id'].attrs['hostname']</span></span>
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<td class="diff-line-num new new_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return None</span></span>
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<td class="diff-line-num new new_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="161" 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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if self.have_metadata is False:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self._get_metadata()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.have_metadata = True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> def get_device_id(self):</span>
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<td class="diff-line-num new new_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> """</span>
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<td class="diff-line-num new new_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> Return the flowcell's device id.</span>
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<td class="diff-line-num new new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> """</span>
</pre>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="170" 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">
170
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if self.have_metadata is False:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._get_metadata()</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.have_metadata = True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" 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">
173
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if self.have_metadata is False:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self._get_metadata()</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.have_metadata = True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> try:</span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> return self.keyinfo['tracking_id'].attrs['device_id']</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="p">@@ -688,13 +688,13 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" 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">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> Return the user supplied sample name</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="181" 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">
181
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> """</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if self.have_metadata is False:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="184" 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">
184
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._get_metadata()</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="185" 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">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.have_metadata = True</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="186" 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">
186
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if self.have_metadata is False:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="187" 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">
187
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self._get_metadata()</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="188" 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">
188
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.have_metadata = True</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="189" 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">
189
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="190" 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">
190
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="191" 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">
191
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> return self.keyinfo['context_tags'].attrs['user_filename_input']</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="192" 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">
192
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Exception, e:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="193" 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">
193
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Exception as e:</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="194" 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">
194
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> return None</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="195" 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">
195
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="196" 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">
196
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="197" 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">
197
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="p">@@ -705,7 +705,7 @@</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="198" 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">
198
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="199" 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">
199
</td>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> table = self.hdf5file[fastq_paths[self.version]['template'] % self.group]</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="200" 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">
200
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> return len(table['Events'][()])</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="201" 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">
201
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Exception, e:</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="202" 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">
202
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Exception as e:</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="203" 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">
203
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> return 0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="204" 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">
204
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="205" 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">
205
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> def get_complement_events_count(self):</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="206" 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">
206
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="p">@@ -715,7 +715,7 @@</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="207" 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">
207
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="208" 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">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> table = self.hdf5file[fastq_paths[self.version]['complement'] % self.group]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="209" 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">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> return len(table['Events'][()])</span>
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<td class="diff-line-num new new_line" data-linenumber="210" 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">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Exception, e:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="211" 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">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Exception as e:</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> return 0</span>
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<td class="diff-line-num new new_line" data-linenumber="213" 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">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="214" 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">
214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> def is_high_quality(self):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="215" 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">
215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="p">@@ -746,7 +746,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="216" 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">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> return 'template'</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="217" 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">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="218" 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">
218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> return 'complement'</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="219" 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">
219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Exception, e:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="220" 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">
220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Exception as e:</span></span>
</pre>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> return None</span>
</pre>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="223" 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">
223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> ####################################################################</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="224" 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">
224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="p">@@ -757,26 +757,26 @@</span></span>
</pre>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> """</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="226" 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">
226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> Return the sequence in the FAST5 file in FASTQ format</span>
</pre>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> """</span>
</pre>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for id, h5path in fastq_paths[self.version].iteritems(): </span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="229" 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">
229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for id, h5path in fastq_paths[self.version].items(): </span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="230" 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">
230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="231" 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">
231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> table = self.hdf5file[h5path % self.group]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="232" 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">
232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> fq = formats.Fastq(table['Fastq'][()])</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="233" 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">
233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> fq.name += " " + self.filename</span>
</pre>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> self.fastqs[id] = fq</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Exception, e:</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Exception as e:</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> pass</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> </span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> def _extract_fastas_from_fast5(self):</span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> """</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> Return the sequence in the FAST5 file in FASTA format</span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> """</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for id, h5path in fastq_paths[self.version].iteritems(): </span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for id, h5path in fastq_paths[self.version].items(): </span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> try:</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> table = self.hdf5file[h5path % self.group]</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> fa = formats.Fasta(table['Fastq'][()])</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> fa.name += " " + self.filename</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> self.fastas[id] = fa</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Exception, e:</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Exception as e:</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> pass</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> </span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> def _extract_template_events(self):</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="p">@@ -786,7 +786,7 @@</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> try:</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> table = self.hdf5file[fastq_paths[self.version]['template'] % self.group]</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> self.template_events = [Event(x) for x in table['Events'][()]]</span>
</pre>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Exception, e:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="260" 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">
260
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Exception as e:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> self.template_events = []</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="262" 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">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> def _extract_complement_events(self):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="264" 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">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="p">@@ -796,7 +796,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="265" 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">
265
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="266" 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">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> table = self.hdf5file[fastq_paths[self.version]['complement'] % self.group]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="267" 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">
267
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> self.complement_events = [Event(x) for x in table['Events'][()]]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="268" 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">
268
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Exception, e:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="269" 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">
269
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Exception as e:</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="270" 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">
270
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> self.complement_events = []</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="271" 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">
271
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="272" 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">
272
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> def _extract_pre_basecalled_events(self):</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="273" 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">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="p">@@ -815,9 +815,9 @@</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="274" 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">
274
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> def _get_metadata(self):</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="275" 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">
275
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> self.keyinfo = self.hdf5file['/UniqueGlobalKey']</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="277" 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">
277
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Exception, e:</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="278" 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">
278
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Exception as e:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="279" 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">
279
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> try:</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="280" 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">
280
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> self.keyinfo = self.hdf5file['/Key']</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="281" 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">
281
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Exception, e:</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="282" 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">
282
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Exception as e:</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="283" 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">
283
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> self.keyinfo = None</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="284" 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">
284
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> logger.warning("Cannot find keyinfo. Exiting.\n")</span>
</pre>
</td>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/formats.py</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/formats.py</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/formats.py</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> phred = ord(score) - 33</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> error_count += 10.0 ** (-phred / 10.0)</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> return error_count / len(self.qual)</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Exception, e:</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Exception as e:</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> return 0.0</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> </span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/times.py</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/times.py</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/times.py</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> from time import strftime, localtime</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="p">@@ -7,10 +7,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> logger = logging.getLogger('poretools')</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> </span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"> def run(parser, args):</span>
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<td class="diff-line-num new new_line" data-linenumber="312" 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">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print '\t'.join(['channel', 'filename', 'read_length', </span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('\t'.join(['channel', 'filename', 'read_length', </span></span>
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<td class="diff-line-num new new_line" data-linenumber="314" 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">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> 'exp_starttime', 'unix_timestamp', 'duration', </span>
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<td class="diff-line-num new new_line" data-linenumber="315" 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">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> 'unix_timestamp_end', 'iso_timestamp', 'day', </span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'hour', 'minute'])</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'hour', 'minute']))</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> </span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> for fast5 in Fast5File.Fast5FileSet(args.files):</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> if fast5.is_open:</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="p">@@ -29,7 +29,7 @@</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"> read_length = 0</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> </span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> lt = localtime(start_time)</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t".join([fast5.get_channel_number(),</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t".join([fast5.get_channel_number(),</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"> fast5.filename, </span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> str(read_length),</span>
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<td class="diff-line-num new new_line" data-linenumber="329" 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">
329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> str(fast5.get_exp_start_time()),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="330" 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">
330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="p">@@ -39,5 +39,5 @@</span></span>
</pre>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> strftime('%Y-%m-%dT%H:%M:%S%z', lt),</span>
</pre>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> strftime('%d', lt),</span>
</pre>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> strftime('%H', lt),</span>
</pre>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strftime('%M', lt)])</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strftime('%M', lt)]))</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> fast5.close()</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/events.py</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/events.py</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/events.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="341" 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">
341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> </span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> def run(parser, args):</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> </span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="p">@@ -7,18 +7,18 @@</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> 'length', 'model_state', 'model_level', 'move', \</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> 'p_model_state', 'mp_model_state', 'p_mp_model_state', \</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> 'p_A', 'p_C', 'p_G', 'p_T', 'raw_index']</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t".join(keys)</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t".join(keys))</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> </span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> if args.pre_basecalled:</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> for fast5 in Fast5File.Fast5FileSet(args.files):</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> for event in fast5.get_pre_basecalled_events(): </span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print '\t'.join([fast5.filename, 'pre_basecalled', str(event)])</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('\t'.join([fast5.filename, 'pre_basecalled', str(event)]))</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> else:</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> for fast5 in Fast5File.Fast5FileSet(args.files):</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> for event in fast5.get_template_events():</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print '\t'.join([fast5.filename, 'template', str(event)]) </span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('\t'.join([fast5.filename, 'template', str(event)])) </span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> for event in fast5.get_complement_events():</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print '\t'.join([fast5.filename, 'complement', str(event)]) </span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('\t'.join([fast5.filename, 'complement', str(event)])) </span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> </span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> fast5.close()</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> </span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/qualdist.py</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/qualdist.py</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/qualdist.py</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> from collections import Counter</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> </span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> def run(parser, args):</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="p">@@ -15,5 +15,5 @@</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> fast5.close()</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> </span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"> for q in qual_count:</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print '\t'.join(str(s) for s in [chr(q+33), q, qual_count[q], </span></span>
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<td class="diff-line-num new new_line" data-linenumber="385" 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">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- total_nucs, float(qual_count[q]) / float(total_nucs)])</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<td class="diff-line-num new new_line" data-linenumber="387" 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">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print ('\t'.join(str(s) for s in [chr(q+33), q, qual_count[q], </span></span>
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<td class="diff-line-num new new_line" data-linenumber="388" 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">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ total_nucs, float(qual_count[q]) / float(total_nucs)]))</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/metadata.py</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/metadata.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="392" 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">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/metadata.py</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> </span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> def run(parser, args):</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"> </span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="p">@@ -6,17 +6,17 @@</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> for i, fast5 in enumerate(Fast5File.Fast5FileSet(args.files)):</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"> for metadata_dict in fast5.read_metadata:</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"> if i == 0:</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- header = metadata_dict.keys()</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t".join(["filename"] + header)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="405" 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">
405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t".join([fast5.filename] + [str( metadata_dict[k] ) for k in header])</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ header = list(metadata_dict.keys())</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t".join(["filename"] + header))</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t".join([fast5.filename] + [str( metadata_dict[k] ) for k in header]))</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "asic_id\tasic_temp\theatsink_temp"</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("asic_id\tasic_temp\theatsink_temp")</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"> for fast5 in Fast5File.Fast5FileSet(args.files):</span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> asic_temp = fast5.get_asic_temp()</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"> asic_id = fast5.get_asic_id()</span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> heatsink_temp = fast5.get_heatsink_temp()</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s\t%s\t%s" % (asic_id, asic_temp, heatsink_temp)</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\t%s\t%s" % (asic_id, asic_temp, heatsink_temp))</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"> fast5.close()</span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/fastq.py</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/fastq.py</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/fastq.py</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"> def run(parser, args):</span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="p">@@ -42,7 +42,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"> args.max_length > 0): </span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"> continue</span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print fa</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(fa)</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"> fast5.close()</span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/occupancy.py</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/occupancy.py</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/occupancy.py</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> from collections import Counter</span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"> import pandas as pd</span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="p">@@ -35,8 +35,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"> pore_values.append(0)</span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"> # make a data frame of the lists</span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- d = {'rownum': range(1,17)*32,</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'colnum': sorted(range(1,33)*16),</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ d = {'rownum': list(range(1,17))*32,</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'colnum': sorted(list(range(1,33))*16),</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"> 'tot_reads': pore_values,</span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"> 'labels': flowcell_layout}</span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"> df = pd.DataFrame(d)</span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"><span class="p">@@ -55,7 +55,7 @@</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"> tot_reads_per_pore = Counter()</span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"> tot_bp_per_pore = Counter()</span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"> </span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t".join(['channel_number', 'start_time', 'duration'])</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t".join(['channel_number', 'start_time', 'duration']))</span></span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"> for fast5 in Fast5File.Fast5FileSet(args.files):</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"> if fast5.is_open:</span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"> fq = fast5.get_fastq()</span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"><span class="p">@@ -70,10 +70,10 @@</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> tot_reads_per_pore[int(pore_id)] += 1</span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"> tot_bp_per_pore[int(pore_id)] += len(fq.seq)</span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"> </span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t".join([</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t".join([</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"> str(pore_id),</span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"> str(start_time),</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- str(fast5.get_duration())])</span></span>
</pre>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ str(fast5.get_duration())]))</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"> fast5.close()</span>
</pre>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"> </span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> if args.plot_type == 'read_count':</span>
</pre>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/index.py</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/index.py</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/index.py</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"> import datetime</span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"> </span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> ############</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"> </span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"> def run(parser, args):</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> </span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "source_filename\ttemplate_fwd_length\tcomplement_rev_length\t2d_length\tasic_id\tasic_temp\theatsink_temp\tchannel\texp_start_time\texp_start_time_string_date\texp_start_time_string_time\tstart_time\tstart_time_string_date\tstart_time_string_time\tduration\tfast5_version"</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("source_filename\ttemplate_fwd_length\tcomplement_rev_length\t2d_length\tasic_id\tasic_temp\theatsink_temp\tchannel\texp_start_time\texp_start_time_string_date\texp_start_time_string_time\tstart_time\tstart_time_string_date\tstart_time_string_time\tduration\tfast5_version")</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"> </span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"> for fast5 in Fast5File.Fast5FileSet(args.files):</span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> </span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"><span class="p">@@ -56,11 +56,11 @@</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> length_complement = len(fastq_reads[1].seq)</span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"> length_2d = len(fastq_reads[2].seq)</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"> </span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % (</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % (</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"> fast5.filename,</span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"> length_template,</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"> length_complement,</span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"> length_2d, </span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- asic_id, asic_temp, heatsink_temp,channel_number,exp_start_time,exp_start_time_string,start_time,start_time_string,duration,fast5_version)</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ asic_id, asic_temp, heatsink_temp,channel_number,exp_start_time,exp_start_time_string,start_time,start_time_string,duration,fast5_version))</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"> </span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"> fast5.close()</span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/readstats.py</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/readstats.py</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/readstats.py</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"><span class="p">@@ -1,8 +1,8 @@</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"> </span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"> def run(parser, args):</span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"> </span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "start_time\tchannel_number\tread_number\ttemplate_events\tcomplement_events"</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("start_time\tchannel_number\tread_number\ttemplate_events\tcomplement_events")</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"> </span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"> for fast5 in Fast5File.Fast5FileSet(args.files):</span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"> </span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"><span class="p">@@ -22,6 +22,6 @@</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> complement_len = 0</span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"> </span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s\t%s\t%s\t%s\t%s" % (start_time, channel_number, read_number, template_len, complement_len)</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\t%s\t%s\t%s\t%s" % (start_time, channel_number, read_number, template_len, complement_len))</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> </span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"> fast5.close()</span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/winner.py</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/winner.py</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/winner.py</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> import sys</span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"> </span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"> #logging</span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"><span class="p">@@ -21,5 +21,5 @@</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> fast5.close()</span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"> </span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"> logger.info("Wow, it's a whopper: your longest read is %d bases." % (longest_size,))</span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print longest_read</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(longest_read)</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"> </span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/stats.py</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="559" 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">
559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/stats.py</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/stats.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="561" 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">
561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import statistics as stat</span></span>
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<td class="diff-line-num new new_line" data-linenumber="563" 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">
563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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<td class="diff-line-num new new_line" data-linenumber="564" 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">
564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import statistics as stat</span></span>
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<td class="diff-line-num new new_line" data-linenumber="565" 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">
565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"> import logging</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"> from collections import defaultdict</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"> logger = logging.getLogger('poretools')</span>
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<td class="diff-line-num new new_line" data-linenumber="569" 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">
569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="p">@@ -14,7 +14,7 @@</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"> fas = fast5.get_fastas_dict()</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"> if len(fas) > 0:</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"> basecalled_files += 1</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for category, fa in fas.iteritems():</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for category, fa in fas.items():</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"> if fa is not None:</span>
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<td class="diff-line-num new new_line" data-linenumber="576" 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">
576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"> stats[category].append(len(fa.seq))</span>
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<td class="diff-line-num new new_line" data-linenumber="577" 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">
577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"> if category == 'twodirections':</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="578" 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">
578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"><span class="p">@@ -23,22 +23,22 @@</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"> </span>
</pre>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"> fast5.close()</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="581" 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">
581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="582" 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">
582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "files\ttotal reads\t%d" % (files)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="583" 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">
583
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "files\ttotal base-called reads\t%d" % (basecalled_files)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="584" 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">
584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("files\ttotal reads\t%d" % (files))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="585" 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">
585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("files\ttotal base-called reads\t%d" % (basecalled_files))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="586" 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">
586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"> for category in sorted(stats.keys()):</span>
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<td class="diff-line-num new new_line" data-linenumber="587" 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">
587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"> sizes = stats[category]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="588" 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">
588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="589" 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">
589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"> if len(sizes) > 0:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="590" 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">
590
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s\ttotal reads\t%d" % (category, len(sizes))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="591" 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">
591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s\ttotal base pairs\t%d" % (category, sum(sizes))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="592" 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">
592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s\tmean\t%.2f" % (category, stat.mean(sizes))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="593" 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">
593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s\tmedian\t%d" % (category, stat.median(sizes))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="594" 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">
594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s\tmin\t%d" % (category, min(sizes))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="595" 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">
595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s\tmax\t%d" % (category, max(sizes))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="596" 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">
596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\ttotal reads\t%d" % (category, len(sizes)))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="597" 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">
597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\ttotal base pairs\t%d" % (category, sum(sizes)))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="598" 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">
598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\tmean\t%.2f" % (category, stat.mean(sizes)))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="599" 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">
599
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\tmedian\t%d" % (category, stat.median(sizes)))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="600" 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">
600
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\tmin\t%d" % (category, min(sizes)))</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="601" 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">
601
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\tmax\t%d" % (category, max(sizes)))</span></span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="602" 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">
602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"> nxvalues = stat.NX(sizes, [25,50,75])</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="603" 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">
603
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s\tN25\t%d" % (category, nxvalues[25])</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="604" 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">
604
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s\tN50\t%d" % (category, nxvalues[50])</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="605" 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">
605
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s\tN75\t%d" % (category, nxvalues[75])</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="606" 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">
606
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\tN25\t%d" % (category, nxvalues[25]))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="607" 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">
607
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\tN50\t%d" % (category, nxvalues[50]))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="608" 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">
608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\tN75\t%d" % (category, nxvalues[75]))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="609" 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">
609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="610" 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">
610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"> logger.warning("No valid sequences observed.\n")</span>
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<td class="diff-line-num new new_line" data-linenumber="611" 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">
611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"> else:</span>
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<td class="diff-line-num new new_line" data-linenumber="612" 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">
612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"><span class="p">@@ -49,15 +49,15 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="613" 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">
613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"> fast5.close()</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="614" 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">
614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="615" 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">
615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"> if len(sizes) > 0:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="616" 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">
616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "total reads\t%d" % (len(sizes))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="617" 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">
617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "total base pairs\t%d" % (sum(sizes))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="618" 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">
618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "mean\t%.2f" % (stat.mean(sizes))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="619" 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">
619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "median\t%d" % (stat.median(sizes))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="620" 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">
620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "min\t%d" % (min(sizes))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="621" 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">
621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "max\t%d" % (max(sizes))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="622" 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">
622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nxvalues = stat.NX(sizes, [25,50,75])</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="623" 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">
623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "N25\t%d" % (nxvalues[25])</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="624" 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">
624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "N50\t%d" % (nxvalues[50])</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="625" 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">
625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "N75\t%d" % (nxvalues[75])</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="626" 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">
626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("total reads\t%d" % (len(sizes)))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="627" 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">
627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("total base pairs\t%d" % (sum(sizes)))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="628" 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">
628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("mean\t%.2f" % (stat.mean(sizes)))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="629" 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">
629
</td>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("median\t%d" % (stat.median(sizes)))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="630" 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">
630
</td>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("min\t%d" % (min(sizes)))</span></span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="631" 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">
631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("max\t%d" % (max(sizes)))</span></span>
</pre>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nxvalues = stat.NX(sizes, [25,50,75])</span></span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("N25\t%d" % (nxvalues[25]))</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("N50\t%d" % (nxvalues[50]))</span></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("N75\t%d" % (nxvalues[75]))</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"> else:</span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"> logger.warning("No valid sequences observed.\n")</span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/nucdist.py</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/nucdist.py</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/nucdist.py</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"> from collections import Counter</span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"> def run(parser, args):</span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"><span class="p">@@ -15,5 +15,5 @@</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"> fast5.close()</span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"> </span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"> for n in nuc_count:</span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print '\t'.join(str(s) for s in [n, nuc_count[n], </span></span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- total_nucs, float(nuc_count[n]) / float(total_nucs)])</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print ('\t'.join(str(s) for s in [n, nuc_count[n], </span></span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ total_nucs, float(nuc_count[n]) / float(total_nucs)]))</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/tabular.py</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/tabular.py</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/tabular.py</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"><span class="p">@@ -1,8 +1,8 @@</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"> </span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"> def run(parser, args):</span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"> </span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print '\t'.join(['length', 'name', 'sequence', 'quals'])</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('\t'.join(['length', 'name', 'sequence', 'quals']))</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"> for fast5 in Fast5File.Fast5FileSet(args.files):</span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"> fqs = fast5.get_fastqs(args.type)</span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"><span class="p">@@ -10,5 +10,5 @@</span></span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"> if fq is None:</span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"> fast5.close()</span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"> continue</span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print '\t'.join([str(len(fq.seq)), fq.name, fq.seq, fq.qual])</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fast5.close()</span></span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print ('\t'.join([str(len(fq.seq)), fq.name, fq.seq, fq.qual]))</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fast5.close()</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/fasta.py</span></span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/fasta.py</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/fasta.py</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"> import sys</span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"> </span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"> def run(parser, args):</span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"><span class="p">@@ -42,7 +42,7 @@</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"> args.max_length > 0): </span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"> continue </span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"> </span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print fa</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(fa)</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"> </span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"> fast5.close()</span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"> </span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/statistics.py</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/statistics.py</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/statistics.py</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"><span class="p">@@ -27,25 +27,25 @@</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"> return None</span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"> </span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"> def NX(l, x=[25,50,75]):</span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Returns NX for all x for a list of numbers l.</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Default: N25, N50, N75</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Assumes all values in list x are between 0 and 100.</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Interpretation: When NX = NX_value, X% of data (in bp) is contained in reads at least NX_value bp long.</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ """</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Returns NX for all x for a list of numbers l.</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Default: N25, N50, N75</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Assumes all values in list x are between 0 and 100.</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Interpretation: When NX = NX_value, X% of data (in bp) is contained in reads at least NX_value bp long.</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ """</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"> if isinstance(l, list) and isinstance(x, list):</span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"> l = sorted(l)</span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"> x = sorted(x)</span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"> total = sum(l)</span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nxsum = 0</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nxvalues = {e:0 for e in x}</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nxsum = 0</span></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nxvalues = {e:0 for e in x}</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"> for e in x:</span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- xpct = total*e/100.0</span></span>
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- while nxsum < xpct and l:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="731" 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">
731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nxsum += l[-1]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="732" 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">
732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- lastsize = l.pop()</span></span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nxvalues[e] = lastsize</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return nxvalues</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ xpct = total*e/100.0</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ while nxsum < xpct and l:</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nxsum += l[-1]</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ lastsize = l.pop()</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nxvalues[e] = lastsize</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return nxvalues</span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="diff"> </span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="diff"> else:</span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="diff"> return None</span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/poretools_main.py</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/poretools_main.py</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/poretools_main.py</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="diff"><span class="p">@@ -13,43 +13,43 @@</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"> </span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="diff"> def run_subtool(parser, args):</span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="diff"> if args.command == 'combine':</span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import combine as submodule</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import combine as submodule</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"> elif args.command == 'events':</span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import events as submodule</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import events as submodule</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"> elif args.command == 'fasta':</span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import fasta as submodule</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import fasta as submodule</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"> elif args.command == 'fastq':</span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import fastq as submodule</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import fastq as submodule</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="diff"> elif args.command == 'hist':</span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import hist as submodule</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import hist as submodule</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"> elif args.command == 'metadata':</span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import metadata as submodule</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import metadata as submodule</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="diff"> elif args.command == 'nucdist':</span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import nucdist as submodule</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import nucdist as submodule</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"> elif args.command == 'occupancy':</span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import occupancy as submodule</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import occupancy as submodule</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff"> elif args.command == 'qualdist':</span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import qualdist as submodule</span></span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import qualdist as submodule</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="diff"> elif args.command == 'qualpos':</span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import qual_v_pos as submodule</span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import qual_v_pos as submodule</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="diff"> elif args.command == 'readstats':</span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import readstats as submodule</span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import readstats as submodule</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="diff"> elif args.command == 'stats':</span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import stats as submodule</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import stats as submodule</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="diff"> elif args.command == 'tabular':</span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import tabular as submodule</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import tabular as submodule</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="diff"> elif args.command == 'times':</span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import times as submodule</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import times as submodule</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="diff"> elif args.command == 'squiggle':</span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import squiggle as submodule</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import squiggle as submodule</span></span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"> elif args.command == 'winner':</span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import winner as submodule</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import winner as submodule</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff"> elif args.command == 'yield_plot':</span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import yield_plot as submodule</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import yield_plot as submodule</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"> elif args.command == 'index':</span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import index as submodule</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import index as submodule</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="diff"> elif args.command == 'organise':</span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import organise as submodule</span></span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import organise as submodule</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff"> </span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="diff"> # run the chosen submodule.</span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="diff"> submodule.run(parser, args)</span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="diff"><span class="p">@@ -57,7 +57,7 @@</span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="diff"> class ArgumentParserWithDefaults(argparse.ArgumentParser):</span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="diff"> def __init__(self, *args, **kwargs):</span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="diff"> super(ArgumentParserWithDefaults, self).__init__(*args, **kwargs)</span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.add_argument("-q", "--quiet", help="Do not output warnings to stderr",</span></span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.add_argument("-q", "--quiet", help="Do not output warnings to stderr",</span></span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="diff"> action="store_true",</span>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="diff"> dest="quiet")</span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="diff"> </span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="diff"><span class="p">@@ -526,12 +526,16 @@</span></span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="diff"> #######################################################</span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="diff"> args = parser.parse_args()</span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="diff"> </span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not args.command:</span></span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ parser.print_help()</span></span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sys.exit(0)</span></span>
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827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="diff"> if args.quiet:</span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="diff"> logger.setLevel(logging.ERROR)</span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="diff"> </span>
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831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="diff"> try:</span>
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<td class="diff-line-num new new_line" data-linenumber="832" 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">
832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="diff"> args.func(parser, args)</span>
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<td class="diff-line-num new new_line" data-linenumber="833" 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">
833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except IOError, e:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="834" 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">
834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except IOError as e:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="835" 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">
835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="diff"> if e.errno != 32: # ignore SIGPIPE</span>
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<td class="diff-line-num new new_line" data-linenumber="836" 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">
836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="diff"> raise</span>
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<td class="diff-line-num new new_line" data-linenumber="837" 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">
837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="838" 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">
838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/combine.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="839" 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">
839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="840" 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">
840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/combine.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="841" 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">
841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/combine.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="842" 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">
842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="843" 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">
843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="diff"> import tarfile</span>
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<td class="diff-line-num new new_line" data-linenumber="844" 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">
844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="diff"> import sys</span>
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<td class="diff-line-num new new_line" data-linenumber="845" 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">
845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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<td class="diff-line-num new new_line" data-linenumber="846" 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">
846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="848" 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">
848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="diff"> #logging</span>
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<td class="diff-line-num new new_line" data-linenumber="849" 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">
849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="diff"> import logging</span>
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<td class="diff-line-num new new_line" data-linenumber="850" 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">
850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/hist.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="851" 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">
851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="852" 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">
852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/hist.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="853" 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">
853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/hist.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="854" 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">
854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="diff"><span class="p">@@ -6,7 +6,7 @@</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="diff"> from matplotlib import pyplot as plt</span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="diff"> </span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="diff"> import seaborn as sns</span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="diff"> </span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="diff"> import logging</span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="diff"> logger = logging.getLogger('poretools')</span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/organise.py</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/organise.py</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/organise.py</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="diff"> import sys</span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="diff"> import os</span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="diff"> from os import makedirs</span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/qual_v_pos.py</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/qual_v_pos.py</span></span>
</pre>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/qual_v_pos.py</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="diff"> from collections import defaultdict</span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="diff"> import pandas</span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="diff"> import matplotlib.pyplot as plt</span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/squiggle.py</span></span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/squiggle.py</span></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/squiggle.py</span></span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="diff"><span class="p">@@ -10,7 +10,7 @@</span></span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="diff"> import logging</span>
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="diff"> logger = logging.getLogger('poretools')</span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="diff"> def plot_squiggle(args, filename, start_times, mean_signals):</span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="diff"> """</span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="diff"><span class="p">@@ -70,7 +70,7 @@</span></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="diff"> </span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="diff"> fast5_set = Fast5File.Fast5FileSet(args.files)</span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="diff"> </span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- first_fast5 = fast5_set.next()</span></span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ first_fast5 = next(fast5_set)</span></span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="diff"> for fast5 in fast5_set:</span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="diff"> # only create a squiggle plot for multiple reads if saving to file.</span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="diff"> if args.saveas is None:</span>
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="diff"><span class="gh" style="color: #999;">Index: poretools-0.6.0+dfsg/poretools/yield_plot.py</span></span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- poretools-0.6.0+dfsg.orig/poretools/yield_plot.py</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ poretools-0.6.0+dfsg/poretools/yield_plot.py</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Fast5File</span></span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Fast5File</span></span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="diff"> import matplotlib</span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="diff"> #matplotlib.use('Agg') # Must be called before any other matplotlib calls</span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="diff"> from matplotlib import pyplot as plt</span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="diff"><span class="p">@@ -25,16 +25,16 @@</span></span>
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="diff"> # compute the cumulative based on reads or total base pairs</span>
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="diff"> if args.plot_type == 'reads':</span>
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918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="diff"> y_label = "Total reads"</span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cumulative = np.cumsum(range(len(start_times)))</span></span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cumulative = np.cumsum(list(range(len(start_times))))</span></span>
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921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="diff"> elif args.plot_type == 'basepairs':</span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="diff"> y_label = "Total base pairs"</span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="diff"> cumulative = np.cumsum(read_lengths)</span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="diff"> </span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="diff"> step = args.skip</span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="diff"> # make a data frame of the lists</span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- d = {'start': [start_times[n] for n in xrange(0, len(start_times), step)],</span></span>
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928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'lengths': [read_lengths[n] for n in xrange(0, len(read_lengths), step)],</span></span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'cumul': [cumulative[n] for n in xrange(0, len(cumulative), step)]}</span></span>
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ d = {'start': [start_times[n] for n in range(0, len(start_times), step)],</span></span>
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931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'lengths': [read_lengths[n] for n in range(0, len(read_lengths), step)],</span></span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'cumul': [cumulative[n] for n in range(0, len(cumulative), step)]}</span></span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="diff"> df = pd.DataFrame(d)</span>
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934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="diff"> </span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="diff"> if args.savedf:</span></pre>
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<a href="https://salsa.debian.org/med-team/poretools/compare/9f6d6dc9b18c2a3db6573f1f8245bc450dd352cc...c025b834827190f6bee251ba994a7288134486a6#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/poretools/compare/9f6d6dc9b18c2a3db6573f1f8245bc450dd352cc...c025b834827190f6bee251ba994a7288134486a6#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,4 +6,4 @@ export LC_ALL=C.UTF-8</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">export PYBUILD_DESTDIR=debian/poretools</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">%:</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">2</span> --buildsystem=pybuild</span></pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">3</span> --buildsystem=pybuild</span></pre>
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