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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/sepp">Debian Med / sepp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/5f269fbe716b0755a3d4e17527258e651eadccc3">5f269fbe</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-10-08T15:55:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Using configuration files per user in ~/.sepp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/bca245584fee812ceb34b7261f1d4f3993043670">bca24558</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-10-08T15:56:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Correcting another wrong file read in the Java part
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/f738f0a11705029996236ef9a70f6af926864e39">f738f0a1</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-10-08T21:49:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Documenting the changes from upstream concerning configuration files
debian/README.source and debian/README.Debian explain what changes have been
made and what the user needs to do.
Manpages have been updated to reflect this.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/eeabe9c4d78184472d262595f03710c78a650537">eeabe9c4</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-10-08T22:16:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Postponing the inclusion of upp until its dependency pasta is packaged
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/5eedbb21645bbbb9bdf522b1ae0b3c00489edac4">5eedbb21</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-10-08T22:19:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Preparing changelog with ITP number
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/05aab011776cfd4a695a212e0d0fe0cd4af18924">05aab011</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-10-09T17:54:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polishing files in debian/ with minor changes
Deleting extra whitespaces
Correcting spelling errors
Using neutral they/their instead of she/her
</pre>
</li>
</ul>
<h4>20 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
<span class="new-file">
+
debian/README.Debian
</span>
</a>
</li>
<li class="file-stats">
<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
<span class="new-file">
+
debian/README.source
</span>
</a>
</li>
<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="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
</a>
</li>
<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
debian/install
</a>
</li>
<li class="file-stats">
<a href="#e705f9c0b5d0a2a928ec403c9867eb9f3c90ae9a">
debian/man/run_abundance.py.1
</a>
</li>
<li class="file-stats">
<a href="#3478ac7e366d3400eb723ca169ed100babf034f5">
debian/man/run_sepp.py.1
</a>
</li>
<li class="file-stats">
<a href="#3410c7cb3f54c55cbccdb8139f0e943f18023a2a">
debian/man/run_tipp.py.1
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</li>
<li class="file-stats">
<a href="#1f3227593f1d0ee63be6cd62d8842e30ff49e220">
debian/man/run_upp.py.1
</a>
</li>
<li class="file-stats">
<a href="#aa12d479aea142d25d0df684ae680d1f71047657">
debian/man/sepp.config.5
</a>
</li>
<li class="file-stats">
<a href="#ca13c5da842c9c77dd19d666915c7a61726b1901">
debian/man/tipp.config.5
</a>
</li>
<li class="file-stats">
<a href="#1e970174edfe922687ab3303f74a4582ba9ee100">
debian/man/upp.config.5
</a>
</li>
<li class="file-stats">
<a href="#46407b1326bdee026280065f20152516ad775d7c">
debian/patches/use_etc_configuration_files.patch
→
debian/patches/configuration_files_in_etc_and_per_user.patch
</a>
</li>
<li class="file-stats">
<a href="#c02e82f4372d47f05f0a2c5371df2f4a919348a4">
debian/patches/looking_for_integer_in_placements.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#81ba44c3c16e24caf31ac9df84839f411079a869">
debian/sepp.manpages
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(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="LC1" class="line" lang="plaintext">README sepp for Debian</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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"></span>
</pre>
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Programs can be run with the Python launcher files placed into /usr/bin.</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></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">Information can be found in the tutorial and readme files written by upstream</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">developers. Those files lie in /usr/share/doc/sepp/ .</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">Yet, the Debian packaging incorporates some changes, mainly concerning</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">configuration files. These are highlighted in the next lines.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></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"></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(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="LC12" class="line" lang="plaintext">Differences to sepp (upstream)</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">------------------------------</span>
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<td class="diff-line-num new new_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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<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">The upstream packaging of sepp includes a file path.config which contains a</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(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="LC16" class="line" lang="plaintext">single line with the directory in which the configuration files lie.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">We have removed this file and instead placed default versions of the</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">configuration files in /etc/sepp/ . These can be overridden by every user by</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">copying them into a .sepp/ directory in their home directory, for instance by</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">executing</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> mkdir ~/.sepp && cp /etc/sepp/*.config ~/.sepp/</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">We have also renamed the upstream file from main.config to sepp.config .</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Tipp: getting the reference dataset and setting things up</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">---------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Tipp uses a reference dataset, which can be found at</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> https://github.com/tandyw/tipp-reference/releases/download/v2.0.0/tipp.zip</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">The user willing to use Tipp should thus download the dataset and either have</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">their system administrator set its path in the [reference] section of tipp.config</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">(see manpage tipp.config(5)) or create their own configuration files as explained</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">above to be able to edit ~/.sepp/tipp.config to put the path to the dataset in</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">the [reference] section.</span></pre>
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<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">We have brought changes to the upstream packaging by not using the path.config</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">file from upstream and instead providing configuration files as conffiles: a</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">default version is placed into /etc/sepp, and every user can make a copy to a</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">dot directory in their home directory in order to be able to edit them. This</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">is explained in debian/README.Debian.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Besides, to be run, tipp depends on a reference dataset that has to be</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">downloaded by the user. Again this is explained in debian/README.Debian.</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">We have not packaged upp for the moment although the effort of preparing it has</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">been made, because its dependency pasta is not packaged yet. As the main</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">functionalities of the package are already brought by sepp and tipp, we think</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">it is worth having sepp and tipp in Debian and adding upp later.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> Thu, 08 Oct 2020 21:57:59 +0200</span></pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">sepp (4.3.10+dfsg-1) UNRELEASED; urgency=medium</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"> * Initial release (Closes: #<span class="idiff left right"><bug></span>)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<span class="idiff left right">971870</span>)</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="LC5" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> <span class="idiff left right">Wed, 07 Oct 2020 21:32:48</span> +0200</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> <span class="idiff left right">Thu, 08 Oct 2020 22:18:43</span> +0200</span></pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -37,9 +37,8 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> libcommons-logging-java,</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> ncbi-blast+</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Description: methods use ensembles of Hidden Markov Models (HMM)</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> The tools SEPP, TIPP, UPP and HIPPI implementing three methods use</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> ensembles of Hidden Markov Models (HMMs) in different ways, each</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> focusing on a different problem.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> The tools SEPP and TIPP implementing these methods use ensembles of Hidden</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> Markov Models (HMMs) in different ways, each focusing on a different problem.</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"> SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> problem of phylogenetic placement of short reads into reference</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">@@ -48,12 +47,3 @@ Description: methods use ensembles of Hidden Markov Models (HMM)</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> TIPP stands for "Taxonomic Identification and Phylogenetic Profiling",</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> and addresses the problem of taxonomic identification and abundance</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> profiling of metagenomic data.</span></pre>
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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="LC52" class="line" lang="plaintext"> UPP stands for "Ultra-large alignments using Phylogeny-aware Profiles",</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> and addresses the problem of alignment of very large datasets,</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> potentially containing fragmentary data. UPP can align datasets with up</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> to 1,000,000 sequences.</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> HIPPI stands for "Highly Accurate Protein Family Classification with</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> Ensembles of HMMs", and addresses the problem of classifying query</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> sequences to protein families.</span></pre>
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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">@@ -14,7 +14,7 @@ License: GPL-3+</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Copyright: 2020 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> 2020 Pierre Gruet <pgtdebian@ree.fr></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> 2020 Pierre Gruet <pgtdebian@<span class="idiff left right">f</span>ree.fr></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">License: GPL-3+</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">License: GPL-3+</span>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.SEPP.md</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">README.TIPP.md</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">README.UPP.md</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"><span class="idiff left right"># </span>README.UPP.md</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">tutorial/sepp-tutorial.md</span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">tutorial/tipp-tutorial.md</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">tutorial/upp-tutorial.md</span></pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><span class="idiff left right"># </span>tutorial/upp-tutorial.md</span></pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">sepp.config etc/sepp</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">tipp.config etc/sepp</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">upp.config etc/sepp</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"><span class="idiff left right"># </span>upp.config etc/sepp</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">tools/merge/*JsonMerger.jar usr/share/sepp/</span></pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#e705f9c0b5d0a2a928ec403c9867eb9f3c90ae9a"><strong>debian/man/run_abundance.py.1</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ run_abundance.py \- helper script to estimate the abundance at a given taxonomic</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">usage: run_abundance.py [\-h] [\-v] [\-A N] [\-P N] [\-F N] [\-\-distance DISTANCE]</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">[\-M DIAMETER] [\-S DECOMP] [\-p DIR] [\-o OUTPUT]</span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">[\-d OUTPUT_DIR] [\-<span class="idiff left right">c CONFIG] [\-</span>t TREE] [\-r RAXML]</span>
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<td class="diff-line-num new old_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="LC8" class="line" lang="plaintext">[\-d OUTPUT_DIR] [\-t TREE] [\-r RAXML]</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">
9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">[\-a ALIGN] [\-f FRAG] [\-m MOLECULE] [\-x N]</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">
10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">[\-cp CHCK_FILE] [\-cpi N] [\-seed N] [\-at N] [\-pt N]</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">[\-g N] [\-b N] [\-bin N] [\-D] [\-C N] [\-G GENES]</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" 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="74" 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">@@ -74,11 +74,6 @@ this info file to set model parameters), a backbone alignment file (in</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext">fasta format), and a fasta file including fragments. The input sequences</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">are assumed to be DNA unless specified otherwise.</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">.TP</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">\fB\-c\fR CONFIG, \fB\-\-config\fR CONFIG</span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">A config file, including options used to run SEPP.</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">Options provided as command line arguments overwrite</span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">config file values for those options. [default: None]</span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">\fB\-t\fR TREE, \fB\-\-tree\fR TREE</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">Input tree file (newick format) [default: None]</span>
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84
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">.TP</span>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#3478ac7e366d3400eb723ca169ed100babf034f5"><strong>debian/man/run_sepp.py.1</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ run_sepp.py \- a phylogenetic placement tool</td>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">usage: run_sepp.py [\-h] [\-v] [\-A N] [\-P N] [\-F N] [\-D DISTANCE] [\-M DIAMETER]</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">.IP</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">[\-S DECOMP] [\-p DIR] [\-o OUTPUT] [\-d OUTPUT_DIR]</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">[\-<span class="idiff left right">c CONFIG] [\-</span>t TREE] [\-r RAXML] [\-a ALIGN] [\-f FRAG]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">[\-t TREE] [\-r RAXML] [\-a ALIGN] [\-f FRAG]</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">[\-m MOLECULE] [\-x N] [\-cp CHCK_FILE] [\-cpi N] [\-seed N]</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">.PP</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">This script runs the SEPP algorithm on an input tree, alignment, fragment</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">@@ -72,11 +72,6 @@ this info file to set model parameters), a backbone alignment file (in</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext">fasta format), and a fasta file including fragments. The input sequences</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext">are assumed to be DNA unless specified otherwise.</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">\fB\-c\fR CONFIG, \fB\-\-config\fR CONFIG</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext">A config file, including options used to run SEPP.</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">Options provided as command line arguments overwrite</span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">config file values for those options. [default: None]</span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">\fB\-t\fR TREE, \fB\-\-tree\fR TREE</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">Input tree file (newick format) [default: None]</span>
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82
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">.TP</span>
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<li id="3410c7cb3f54c55cbccdb8139f0e943f18023a2a">
<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#3410c7cb3f54c55cbccdb8139f0e943f18023a2a"><strong>debian/man/run_tipp.py.1</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">@@ -5,13 +5,20 @@ run_tipp.py \- an identification and phylogenetic profiling tool</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">usage: run_tipp.py [\-h] [\-v] [\-A N] [\-P N] [\-F N] [\-\-distance DISTANCE]</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">[\-M DIAMETER] [\-S DECOMP] [\-p DIR] [\-o OUTPUT]</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">[\-d OUTPUT_DIR] [\-<span class="idiff left right">c CONFIG] [\-</span>t TREE] [\-r RAXML] [\-a ALIGN]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">[\-d OUTPUT_DIR] [\-t TREE] [\-r RAXML] [\-a ALIGN]</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">[\-f FRAG] [\-m MOLECULE] [\-x N] [\-cp CHCK_FILE] [\-cpi N]</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">[\-seed N] [\-R N] [\-at N] [\-D] [\-pt N] [\-PD N]</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">[\-tx TAXONOMY] [\-txm MAPPING] [\-adt TREE] [\-C N]</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">This script runs the SEPP algorithm on an input tree, alignment, fragment</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">file, and RAxML info file.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">file, and RAxML info file. It uses a reference dataset which has to be</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">downloaded from</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fBhttps://github.com/tandyw/tipp-reference/releases/download/v2.0.0/tipp.zip\fR</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">If the local administrator has not set the path to this reference dataset in</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">/etc/sepp/tipp.config, you should copy this file to ~/.sepp/ and put the path</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">to the dataset in the \fBreference\fR section of the configuration file,</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">see \fBtipp.config\fR(5).</span>
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15
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">.SS "optional arguments:"</span>
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16
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">.TP</span>
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17
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</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">@@ -74,11 +81,6 @@ this info file to set model parameters), a backbone alignment file (in</td>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">fasta format), and a fasta file including fragments. The input sequences</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext">are assumed to be DNA unless specified otherwise.</span>
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76
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext">.TP</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">\fB\-c\fR CONFIG, \fB\-\-config\fR CONFIG</span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">A config file, including options used to run SEPP.</span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">Options provided as command line arguments overwrite</span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">config file values for those options. [default: None]</span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">.TP</span>
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82
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext">\fB\-t\fR TREE, \fB\-\-tree\fR TREE</span>
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83
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext">Input tree file (newick format) [default: None]</span>
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84
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext">.TP</span>
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<li id="1f3227593f1d0ee63be6cd62d8842e30ff49e220">
<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#1f3227593f1d0ee63be6cd62d8842e30ff49e220"><strong>debian/man/run_upp.py.1</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">@@ -6,7 +6,7 @@ usage: run_upp.py [\-h] [\-v] [\-F N] [\-D DISTANCE] [\-\-diameter DIAMETER]</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">.IP</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">[\-p DIR] [\-o OUTPUT] [\-d OUTPUT_DIR] [\-m MOLECULE] [\-x N]</span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">[\-cp CHCK_FILE] [\-cpi N] [\-seed N] [\-A N] [\-M N] [\-T N]</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">[\-B N] [\-S DECOMP] [\-s SEQ] [\-<span class="idiff left right">c CONFIG] [\-</span>t TREE] [\-a ALIGN]</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">[\-B N] [\-S DECOMP] [\-s SEQ] [\-t TREE] [\-a ALIGN]</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">[\-l N] [\-P N] [\-r RAXML] [\-f FRAG]</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">.PP</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">This script runs the UPP algorithm on set of sequences. A backbone alignment</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">@@ -95,11 +95,6 @@ alignment is given, the sequence file will be randomly</td>
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95
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext">split into a backbone set (size set to B) and query</span>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext">set (remaining sequences), [default: None]</span>
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97
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">.TP</span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext">\fB\-c\fR CONFIG, \fB\-\-config\fR CONFIG</span>
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<td class="diff-line-num old old_line" data-linenumber="99" 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">
99
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<td class="diff-line-num new_line old" data-linenumber="98" 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="LC99" class="line" lang="plaintext">A config file, including options used to run UPP.</span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext">Options provided as command line arguments overwrite</span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext">config file values for those options. [default: None]</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext">.TP</span>
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103
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext">\fB\-t\fR TREE, \fB\-\-tree\fR TREE</span>
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104
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">Input tree file (newick format) [default: None]</span>
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105
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">.TP</span>
</pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#aa12d479aea142d25d0df684ae680d1f71047657"><strong>debian/man/sepp.config.5</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="130" 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>
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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">@@ -130,6 +130,11 @@ A string, indicating the name of the placer to use. Currently only \fB"pplacer"\</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext">A boolean \fBTrue\fR or \fBFalse\fR, indicating whether to apply weights while caring for fragments or not.</span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext">.RE</span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">.SH FILES</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">\fB/etc/sepp/sepp.config\fR</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">\fB~/.sepp/sepp.config\fR, if existing, overrides the one in /etc/sepp.</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"></span>
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133
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext">.SH "SEE ALSO"</span>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext">.PP</span>
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135
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext">\fBrun_sepp.py\fR(1)</span></pre>
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<li id="ca13c5da842c9c77dd19d666915c7a61726b1901">
<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#ca13c5da842c9c77dd19d666915c7a61726b1901"><strong>debian/man/tipp.config.5</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" 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="159" 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">@@ -159,6 +159,11 @@ The section begins with \fB[tipp]\fR, and it has the following field:</td>
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159
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext">An boolean \fBtrue\fR or \fBfalse\fR, currently not used.</span>
</pre>
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160
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext">.RE</span>
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161
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">.SH FILES</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">\fB/etc/sepp/tipp.config\fR</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">.PP</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">\fB~/.sepp/tipp.config\fR, if existing, overrides the one in /etc/sepp.</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"></span>
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162
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext">.SH "SEE ALSO"</span>
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163
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="plaintext">.PP</span>
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164
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext">\fBrun_tipp.py\fR(1)</span></pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#1e970174edfe922687ab3303f74a4582ba9ee100"><strong>debian/man/upp.config.5</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" 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="140" 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">@@ -140,6 +140,11 @@ The string \fBrun_pasta.py\fR, pointing to the PASTA program, which has to be</td>
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140
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext">in the PATH.</span>
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141
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext">.RE</span>
</pre>
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142
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext"></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">.SH FILES</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">\fB/etc/sepp/upp.config\fR</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="plaintext">.PP</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="plaintext">\fB~/.sepp/upp.config\fR, if existing, overrides the one in /etc/sepp.</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"></span>
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143
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext">.SH "SEE ALSO"</span>
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144
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext">.PP</span>
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145
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext">\fBrun_upp.py\fR(1)</span></pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#46407b1326bdee026280065f20152516ad775d7c"><strong>debian/patches/use_etc_configuration_files.patch</strong>
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<strong>debian/patches/configuration_files_in_etc_and_per_user.patch</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: using configuration files that are in /etc</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: using configuration files that are in /etc<span class="idiff left right"> or in ~/.sepp</span></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-<span class="idiff left right">09-19</span></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-<span class="idiff left right">10-08</span></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/run_tipp_tool.py</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/run_tipp_tool.py</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -43,<span class="idiff left right">9 +43,7</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -43,<span class="idiff left right">10 +43,11</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> return args</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-root_p = open(os.path.join(os.path.split(</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.path.split(sepp.__file__)[0])[0], "home.path")).readlines()[0].strip()</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-tipp_config_path = os.path.join(root_p, "tipp.config")</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+tipp_config_path = "/etc/sepp/tipp.config"</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+home = os.path.expanduser("~")</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if os.path.isfile(home + "/.sepp/tipp.config"):</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;">+ tipp_config_path = home + "/.sepp/tipp.config"</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else:</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tipp_config_path = "/etc/sepp/tipp.config"</span></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"> def profile(input, gene, output, prefix, threshold):</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> sepp.config.set_main_config_path(tipp_config_path)</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;">--- a/sepp/config.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;">+++ b/sepp/config.py</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="p">@@ -48,<span class="idiff left right">9 +48,7</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -48,<span class="idiff left right">10 +48,11</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> _LOG = get_logger(__name__)</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> </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;">-root_p = open(os.path.join(os.path.split(</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;">- os.path.split(__file__)[0])[0], "home.path")).readlines()[0].strip()</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-main_config_path = os.path.join(root_p, "main.config")</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+main_config_path = "/etc/sepp/sepp.config"</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+home = os.path.expanduser("~")</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if os.path.isfile(home + "/.sepp/sepp.config"):</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ main_config_path = home + "/.sepp/sepp.config"</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else:</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ main_config_path = "/etc/sepp/sepp.config"</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> def set_main_config_path(filename):</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> global main_config_path</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/sepp/ensemble.py</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/sepp/ensemble.py</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="p">@@ -161,7 +161,<span class="idiff left right">7</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -161,7 +161,<span class="idiff left right">11</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> def augment_parser():</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sepp.config.set_main_config_path(os.path.expanduser("~/.sepp/upp.config"))</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sepp.config.set_main_config_path("/etc/sepp/upp.config")</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ home = os.path.expanduser("~")</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if os.path.isfile(home + "/.sepp/upp.config"):</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sepp.config.set_main_config_path(home + "/.sepp/upp.config")</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else:</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sepp.config.set_main_config_path("/etc/sepp/upp.config")</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> parser = sepp.config.get_parser()</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> parser.description = (</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> "This script runs the UPP algorithm on set of sequences. A backbone "</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/sepp/exhaustive_tipp.py</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/sepp/exhaustive_tipp.py</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="p">@@ -483,12 +483,<span class="idiff left right">7</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -483,12 +483,<span class="idiff left right">11</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> def augment_parser():</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" 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="66" 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">@@ -52,20 +66,28 @@ Last-Update: 2020-09-19</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.path.split(</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __file__)[0])[0], "home.path")).readlines()[0].strip()</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tipp_config_path = os.path.join(root_p, "tipp.config")</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;">+ tipp_config_path = "/etc/sepp/tipp.config"</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ home = os.path.expanduser("~")</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if os.path.isfile(home + "/.sepp/tipp.config"):</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tipp_config_path = home + "/.sepp/tipp.config"</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else:</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tipp_config_path = "/etc/sepp/tipp.config"</span></span>
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56
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> sepp.config.set_main_config_path(tipp_config_path)</span>
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57
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> # default_settings['DEF_P'] = (100 ,</span>
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58
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> # "Number of taxa (i.e. no decomposition)")</span>
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59
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/sepp/exhaustive_upp.py</span></span>
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60
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/sepp/exhaustive_upp.py</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="p">@@ -324,9 +324,<span class="idiff left right">7</span> @@</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="p">@@ -324,9 +324,<span class="idiff left right">11</span> @@</span></span>
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62
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"> </span>
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63
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"> </span>
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64
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"> def augment_parser():</span>
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65
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- root_p = open(os.path.join(os.path.split(</span></span>
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66
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.path.split(__file__)[0])[0], "home.path")).readlines()[0].strip()</span></span>
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67
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- upp_config_path = os.path.join(root_p, "upp.config")</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ upp_config_path = "/etc/sepp/upp.config"</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ home = os.path.expanduser("~")</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if os.path.isfile(home + "/.sepp/upp.config"):</span></span>
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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;">+ upp_config_path = home + "/.sepp/upp.config"</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else:</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ upp_config_path = "/etc/sepp/upp.config"</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="diff"> sepp.config.set_main_config_path(upp_config_path)</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="diff"> parser = sepp.config.get_parser()</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="diff"> parser.description = (</span></pre>
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<li id="c02e82f4372d47f05f0a2c5371df2f4a919348a4">
<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#c02e82f4372d47f05f0a2c5371df2f4a919348a4"><strong>debian/patches/looking_for_integer_in_placements.patch</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">@@ -4,7 +4,7 @@ Description: looking for the right index in placements JSONArray</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> for the right position.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">Forwarded: https://github.com/smirarab/sepp/issues/86</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">Last-Update: 2020-10-0<span class="idiff left right">5</span></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Last-Update: 2020-10-0<span class="idiff left right">8</span></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">--- a/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java</span></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">@@ -30,3 +30,29 @@ Last-Update: 2020-10-05</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> if (pr.getDouble(3) > ((Double) mainEdgeLen.get(newLab))</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> .doubleValue())</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/merge/src/phylolab/taxonamic/JSONMerger.java</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/merge/src/phylolab/taxonamic/JSONMerger.java</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -205,6 +205,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> HashMap < String, String > labelMap = mapTreeBranchNames(jsonTree, originalTree);</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> JSONArray placements = json.getJSONArray("placements");</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ JSONArray fields = json.getJSONArray("fields");</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int locEdgeNum=0;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ while (! fields.getString(locEdgeNum).equals("edge_num")) {</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ locEdgeNum++;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> for (Iterator < JSONObject > iterator = placements.iterator(); iterator.hasNext();) {</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> JSONObject placement = iterator.next();</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="p">@@ -254,8 +260,8 @@</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> /*</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> * Adjust the placement edge label</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> */</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String newLab = (String) labelMap.get(precord.getString(0));</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- newRecord.set(0, new Integer(newLab));</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String newLab = (String) labelMap.get(precord.getString(locEdgeNum));</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;">+ newRecord.set(locEdgeNum, new Integer(newLab));</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> /*</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> * Adjust edge length values to correspond to somewhere on the main tree.</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> * TODO: This is pretty bad. We should fix this.</span></pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -3,7 +3,7 @@ use_debian_packaged_guppy_from_pplacer.patch</td>
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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">change_java_version_for_ant.patch</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">json_collections.patch</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="plaintext">java_build.patch</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">use_etc_configuration_files</span>.patch</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">configuration_files_in_etc_and_per_user</span>.patch</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="plaintext">looking_for_integer_in_placements.patch</span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">deactivating_log_test.patch</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">make_split_sequences_script.patch</span>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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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="LC3" 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="LC5" 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="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" 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>
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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">@@ -61,6 +48,9 @@ override_dh_auto_install:</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> # not really part of the software but instead a helper script.</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> mkdir -p debian/sepp/usr/share/sepp</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> mv debian/sepp/usr/bin/split_sequences.py debian/sepp/usr/share/sepp</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="LC52" class="line" lang="plaintext"> # Not installing upp for now.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> $(RM) debian/sepp/usr/bin/run_upp.py</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"># To test, we move the test tree into a subdir of /tmp and we proceed to the</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"># following changes:</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -86,5 +76,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"> PYTHONPATH=$$PYTHONPATH:../../ python3 -m unittest discover -v</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"># Invoking dh_installman with --language=C to get "traditional" manpages</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"># although the files we put in /usr/bin end with ".py".</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">override_dh_installman:</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> dh_installman --language=C</span></pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#81ba44c3c16e24caf31ac9df84839f411079a869"><strong>debian/sepp.manpages</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/man/*.1</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">debian/man/*.5</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/man/run_abundance.py.1</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/man/run_sepp.py.1</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/man/run_tipp.py.1</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/man/run_tipp_tool.py.1</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"># debian/man/run_upp.py.1</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">debian/man/sepp.config.5</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">debian/man/tipp.config.5</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"># debian/man/upp.config.5</span></pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/f625ecdfe81b837b16ba9081941187688a2bc813...05aab011776cfd4a695a212e0d0fe0cd4af18924#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right"> </span>version=4</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</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">opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">https://github.com/smirarab/sepp//releases .*/archive/v?@ANY_VERSION@\.tar\.gz</span></pre>
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