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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/tombo">Debian Med / tombo</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/a9aa99dd2fed4f35ad6bcf60b4e175c89aedbc97">a9aa99dd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T10:16:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">python3-mappy now available
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/84951c86cbc28736d3336f1b0761a5379b5c517c">84951c86</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T11:29:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/63a6543e882364ddff4b6c0b3190b4227d821f9a">63a6543e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T11:30:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install scripts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/04329a29017f9459eca0ff42ae77dfe0e26c0b8b">04329a29</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T11:38:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add doc
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/3512b4d6f806a150e18e92f003fc72c7fa617aa7">3512b4d6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T11:41:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix permissions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/afd96d31d7825c5f7c7c781a58699724296bb153">afd96d31</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T11:44:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add recommends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/ad9c86176950e371b406ce5574af7286c342d93a">ad9c8617</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T13:22:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Create sphinx documentation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/c636df781a093dcec1f65b0b947a54c048bf725b">c636df78</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T13:35:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtest at least for the help system
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/82860e08ee4d14bdc8d4a2f927a426e61c05dc78">82860e08</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T13:43:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Typo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/ca75c3b47b1c01d20e72d83163a242608eb38266">ca75c3b4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T13:54:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Separate doc package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/4f46e416a090c7987bda90f6eb62217a3b8b8973">4f46e416</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T13:55:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DEP3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/fdd6753c4d9d57da3c9c8e6638187f40bd6aa6b4">fdd6753c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T14:30:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Syntax
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/985705ae16b0771ccb7394e155d1f23d2650389a">985705ae</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T14:30:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix installation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/fbc2a8517f345ae9e1ace59ad378091de44f141c">fbc2a851</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T14:30:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix section
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/e894e3514544dee2259f55ea84db3bd9c46f7f3a">e894e351</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T14:31:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try hardening
</pre>
</li>
</ul>
<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</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="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#1d2a6c0c9f28e89358b99c47654277b227c6ce5b">
debian/patches/no_future.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
<li class="file-stats">
<a href="#ec21bc3fc0d6c40bf60d38cffbc8bb9ce210708b">
<span class="new-file">
+
debian/tombo-doc.doc-base
</span>
</a>
</li>
<li class="file-stats">
<a href="#63b7da0ee55f04d4ca46537884ef38ce06df3104">
<span class="new-file">
+
debian/tombo-doc.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#65ab268091913b7d0d4090d2cd674dcbcb7abb65">
<span class="new-file">
+
debian/tombo.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#2c0c6e0a4eb86f24de89802f6e0bd2c801b142e1">
<span class="new-file">
+
debian/tombo.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#791ff611a35b3170ce5364ebeb4fb2881aad91a0">
<span class="new-file">
+
debian/tombo.manpages
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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1
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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">tombo (1.5.1-1) UNRELEASED; urgency=medium</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<bug>)</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4
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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> TODO: python3-mappy (from minimap2)</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> blocked by https://salsa.debian.org/med-team/ksw2</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="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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #963596)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 15 Jun 2020 11:13:59 +0200</span></pre>
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<br>
</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,8 +8,16 @@ Build-Depends: debhelper-compat (= 13),</td>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3-all-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> cython3,</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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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> python3-numpy,</span>
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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> python3-tqdm</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> sphinx-doc,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python3-sphinx,</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> python3-sphinx-rtd-theme,</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> python3-sphinx-argparse,</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> python3-h5py <!nocheck>,</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> python3-mappy <!nocheck>,</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> python3-numpy <!nocheck>,</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> python3-scipy <!nocheck>,</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> python3-tqdm <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> python3-nose2 <!nocheck></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/tombo</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/tombo.git</span>
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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">@@ -21,11 +29,25 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> python3-h5py,</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> python3-mappy,</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> python3-numpy,</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> python3-scipy,</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> python3-mappy,</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> python3-tqdm</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Recommends: python3-pyfaidx,</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> python3-rpy2</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Description: identification of modified nucleotides from raw nanopore sequencing data</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> Tombo is a suite of tools primarily for the identification of modified</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> nucleotides from nanopore sequencing data. Tombo also provides tools for</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> the analysis and visualization of raw nanopore signal.</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Package: tombo-doc</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Section: doc</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Depends: ${sphinxdoc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Description: identification of modified nucleotides from raw nanopore sequencing data (doc)</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> Tombo is a suite of tools primarily for the identification of modified</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> nucleotides from nanopore sequencing data. Tombo also provides tools for</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> the analysis and visualization of raw nanopore signal.</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> This package contains the documentation for tombo.</span></pre>
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<a href="https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -48,7 +48,6 @@ License: BSD-3-clause</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">Comment:</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> You are under no obligation whatsoever to provide any bug fixes,</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> patches, or upgrades to the features, functionality or performance of</span>
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<a href="https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PROGNAME</span><span class="k" style="font-weight: 600;">}</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.manpages</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<li id="1d2a6c0c9f28e89358b99c47654277b227c6ce5b">
<a href="https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a#1d2a6c0c9f28e89358b99c47654277b227c6ce5b"><strong>debian/patches/no_future.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">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 15 Jun 2020 11:13:59 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Do not require future since we are using Python3 anyway</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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1
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/setup.py</span>
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2
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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3
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">@@ -1,4 +1,3 @@</span></span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># this provides:</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># DEB_SOURCE: the source package name</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM: the package's upstream version</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"># SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"># specified by <https://reproducible-builds.org/specs/source-date-epoch/></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"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">export http_proxy='127.0.0.1:9'</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</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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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> dh $@ --with python3,sphinxdoc --buildsystem=pybuild</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">overide_dh_fixperms:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> dh_fixperms</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> find debian -name "*.model" -exec chmod -x \{\} \;</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">override_dh_auto_build:</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> sphinx-build -N -bhtml docs docs/build</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="LC23" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">#override_dh_auto_test:</span>
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25
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"># do_stuff_for_testing</span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></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="shell"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#PACKAGENAME#</span></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">tombo</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span></pre>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"********* Testing help commands **********</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">tombo <span class="nt" style="color: #000080;">-h</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">{</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Main tombo help failed. Likely a syntax error.'</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span> <span class="o" style="font-weight: 600;">}</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">tombo resquiggle <span class="nt" style="color: #000080;">-h</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">tombo preprocess annotate_raw_with_fastqs <span class="nt" style="color: #000080;">-h</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">tombo filter clear_filters <span class="nt" style="color: #000080;">-h</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">tombo filter stuck <span class="nt" style="color: #000080;">-h</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">tombo filter level_coverage <span class="nt" style="color: #000080;">-h</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">tombo filter q_score <span class="nt" style="color: #000080;">-h</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">tombo filter raw_signal_matching <span class="nt" style="color: #000080;">-h</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">tombo filter genome_locations <span class="nt" style="color: #000080;">-h</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell">tombo detect_modifications de_novo <span class="nt" style="color: #000080;">-h</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">tombo detect_modifications alternative_model <span class="nt" style="color: #000080;">-h</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell">tombo detect_modifications model_sample_compare <span class="nt" style="color: #000080;">-h</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">tombo detect_modifications level_sample_compare <span class="nt" style="color: #000080;">-h</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">tombo detect_modifications aggregate_per_read_stats <span class="nt" style="color: #000080;">-h</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">tombo text_output browser_files <span class="nt" style="color: #000080;">-h</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell">tombo text_output signif_sequence_context <span class="nt" style="color: #000080;">-h</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">tombo plot max_coverage <span class="nt" style="color: #000080;">-h</span></span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell">tombo plot genome_locations <span class="nt" style="color: #000080;">-h</span></span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell">tombo plot motif_centered <span class="nt" style="color: #000080;">-h</span></span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell">tombo plot max_difference <span class="nt" style="color: #000080;">-h</span></span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell">tombo plot most_significant <span class="nt" style="color: #000080;">-h</span></span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell">tombo plot motif_with_stats <span class="nt" style="color: #000080;">-h</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell">tombo plot per_read <span class="nt" style="color: #000080;">-h</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell">tombo plot roc <span class="nt" style="color: #000080;">-h</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell">tombo plot per_read_roc <span class="nt" style="color: #000080;">-h</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell">tombo plot kmer <span class="nt" style="color: #000080;">-h</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell">tombo plot cluster_most_significant <span class="nt" style="color: #000080;">-h</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell">tombo build_model estimate_scale <span class="nt" style="color: #000080;">-h</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell">tombo build_model event_resquiggle <span class="nt" style="color: #000080;">-h</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell">tombo build_model estimate_reference <span class="nt" style="color: #000080;">-h</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell">tombo build_model estimate_alt_reference <span class="nt" style="color: #000080;">-h</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="sh" style="color: #d14;">This test only tests the help system</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="sh" style="color: #d14;">There is an extensive test in </span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="sh" style="color: #d14;"> tombo/tests/shell_tests.sh</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="sh" style="color: #d14;">but this requires to download larger data</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="sh" style="color: #d14;">sets which is not done for the moment.</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a#ec21bc3fc0d6c40bf60d38cffbc8bb9ce210708b"><strong>debian/tombo-doc.doc-base</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Document: tombo</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Title: documentation for tombo</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Author: Oxford Nanopore Technologies Ltd.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Abstract: identification of modified nucleotides from raw nanopore sequencing data</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Tombo is a suite of tools primarily for the identification of modified</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> nucleotides from nanopore sequencing data. Tombo also provides tools for</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> the analysis and visualization of raw nanopore signal.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Section: Science/{Biology,Medicine} # see /usr/share/doc/doc-base/doc-base.txt.gz "2.3.3. The `section' field"</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Format: html</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Index: /usr/share/doc/tombo/html/index.html</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Files: /usr/share/doc/tombo/html/*</span></pre>
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<a href="https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a#63b7da0ee55f04d4ca46537884ef38ce06df3104"><strong>debian/tombo-doc.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">docs</span><span class="o" style="font-weight: 600;">/</span><span class="nx">build</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tombo</span><span class="o" style="font-weight: 600;">/</span><span class="nx">html</span></span></pre>
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<a href="https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a#65ab268091913b7d0d4090d2cd674dcbcb7abb65"><strong>debian/tombo.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH TOMBO "1" "June 2020" "tombo 1.5.1" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">tombo \- identification of modified nucleotides from raw nanopore sequencing data</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B tombo</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\-h] [\-v]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">{resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot}</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">\&...</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Tombo also provides tools for the analysis and visualization of raw nanopore signal.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.SH "Tombo command groups (additional help available within each command group):"</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">resquiggle</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Re\-annotate raw signal with genomic alignment from existing basecalls.</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">preprocess</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Pre\-process nanopore reads for Tombo processing.</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">filter</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Apply filter to Tombo index file for specified criterion.</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">detect_modifications</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Perform statistical testing to detect non\-standard nucleotides.</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.TP</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">text_output</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Output Tombo results in text files.</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.TP</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">build_model</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Create canonical and alternative base Tombo models.</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.TP</span>
</pre>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">plot</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Save plots to visualize raw nanopore signal or testing results.</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.SS "optional arguments:"</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.TP</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">show this help message and exit</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.TP</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-v\fR, \fB\-\-version\fR</span>
</pre>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">show Tombo version and exit.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a#2c0c6e0a4eb86f24de89802f6e0bd2c801b142e1"><strong>debian/tombo.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">usr</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">scripts</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tombo</span></span></pre>
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<a href="https://salsa.debian.org/med-team/tombo/-/compare/160286781eb4373ae63afcf7b9a84a89c9700a4f...e894e3514544dee2259f55ea84db3bd9c46f7f3a#791ff611a35b3170ce5364ebeb4fb2881aad91a0"><strong>debian/tombo.manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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