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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/ragout">Debian Med / ragout</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ragout/commit/1a3e937151ac69409affacc682d93e15dd8480e2">1a3e9371</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-02-15T10:37:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Package with example data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ragout/commit/7ebcf2b6267c9be127c770f1a8468f652ae7d0e6">7ebcf2b6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-02-15T12:13:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ragout/commit/c6ae4859f5fe9a7dedd482df3b861e47c08a1900">c6ae4859</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-02-15T12:29:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">install newick
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ragout/commit/b1fcb230f6b4dc696c1d4aa8111f0a625024aab6">b1fcb230</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-02-15T13:25:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Manpages, autopkgtest
</pre>
</li>
</ul>
<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#adfbeabbb44ac6c611fbd7b40716d10fe8743309">
<span class="new-file">
+
debian/patches/install_newick.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
</span>
</a>
</li>
<li class="file-stats">
<a href="#ff985fa0cc2993a40ac1864d33d34e720e62d58c">
<span class="new-file">
+
debian/ragout-examples.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#25612e51947f40549be14413f0123a318917bb1e">
<span class="new-file">
+
debian/ragout-maf2synteny.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#8927f2ecb4b13b3cc97662b867fab8b736e0e8c2">
<span class="new-file">
+
debian/ragout-overlap.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#1a6bd62237f1b57d96aa452beda82a2b2fa10177">
<span class="new-file">
+
debian/ragout.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#5eaab3a6d332a70f8f7ab5b488590b063dc6f4c8">
<span class="new-file">
+
debian/ragout.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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="16" 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">@@ -16,7 +16,9 @@ Package: ragout</td>
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<td class="diff-line-num old_line" data-linenumber="16" 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">
16
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: any</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> ${python:Depends},</span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> ${misc:Depends}</span>
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<td class="diff-line-num new old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> ${misc:Depends},</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> sibelia,</span>
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<td class="diff-line-num new old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python-networkx</span>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Description: Reference-Assisted Genome Ordering UTility</span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> Ragout (Reference-Assisted Genome Ordering UTility) is a tool for</span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> chromosome-level scaffolding using multiple references. Given initial</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" 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="33" 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">@@ -31,3 +33,25 @@ Description: Reference-Assisted Genome Ordering UTility</td>
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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> Ragout now supports both small and large genomes (of mammalian scale</span>
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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> and complexity). The assembly of highly polymorphic genomes is</span>
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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> currently limited.</span>
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(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="LC36" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(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="LC37" class="line" lang="plaintext">Package: ragout-examples</span>
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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(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="LC38" class="line" lang="plaintext">Architecture: all</span>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(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="LC39" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(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="LC40" class="line" lang="plaintext"> ${python:Depends},</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Description: Reference-Assisted Genome Ordering UTility (example data)</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> Ragout (Reference-Assisted Genome Ordering UTility) is a tool for</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> chromosome-level scaffolding using multiple references. Given initial</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> assembly fragments (contigs/scaffolds) and one or multiple related</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> references (complete or draft), it produces a chromosome-scale assembly</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> (as a set of scaffolds).</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> The approach is based on the analysis of genome rearrangements (like</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> inversions or chromosomal translocations) between the input genomes and</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> reconstructing the most parsimonious structure of the target genome.</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> Ragout now supports both small and large genomes (of mammalian scale</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> and complexity). The assembly of highly polymorphic genomes is</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> currently limited.</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"> This package contains example data to test ragout.</span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,9 +4,52 @@ Source: https://github.com/fenderglass/Ragout/releases</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Files-Excluded: lib/networkx</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Copyright: 20xx-20yy <upstream></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">License: <license></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Copyright: 2013-2018 Mikhail Kolmogorov and Joel Armstrong and</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Brian J. Raney and Ian Streeter and Matthew Dunn and</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Fengtang Yang and Duncan Odom and Paul Flicek and</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Thomas M. Keane and David Thybert and</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> Benedict Paten and Son Pham</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">License: BSD-3-clause</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Files: lib/newick/*</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Copyright: 2003-2008 Thomas Mailund <mailund@birc.au.dk></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">License: GPL-2+</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> This program is free software; you can redistribute it and/or modify</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> it under the terms of the GNU General Public License as published by</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> the Free Software Foundation; either version 2 of the License, or</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> (at your option) any later version.</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> .</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> This program is distributed in the hope that it will be useful,</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> GNU General Public License for more details.</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> .</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> On Debian systems you can find the full text of the GNU General Public</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> License at /usr/share/common-licenses/GPL-2.</span>
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9
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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10
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Files: debian/*</span>
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11
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Copyright: 2019 Andreas Tille <tille@debian.org></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">License: <license></span></pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">License: BSD-3-clause</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">License: BSD-3-clause</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> Redistribution and use in source and binary forms, with or without</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> modification, are permitted provided that the following conditions are met:</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> * Redistributions of source code must retain the above copyright</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> notice, this list of conditions and the following disclaimer.</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> * Redistributions in binary form must reproduce the above copyright</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> notice, this list of conditions and the following disclaimer in the</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> documentation and/or other materials provided with the distribution.</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> * Neither the name of the authors nor the</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> names of contributors may be used to endorse or promote products</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> derived from this software without specific prior written permission.</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> .</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> DISCLAIMED. IN NO EVENT SHALL AUTHORS BE LIABLE FOR ANY</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></pre>
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<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: teal;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> <span class="nv" style="color: teal;">$MANDIR</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: teal;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: navy;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: teal;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: navy;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: teal;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: teal;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PROGNAME</span><span class="k" style="font-weight: 600;">}</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Chromosome assembly with multiple references"</span> <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>ragout-maf2synteny</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>ragout-overlap</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Constructs overlap graph from input contigsand outputs it in dot format"</span> <span class="se" style="color: #d14;">\</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">EOT</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="no" style="color: teal;">EOT</span></span></pre>
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<li id="68e0b13744e158347bfd74ebaaca667435f07d14">
<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#adfbeabbb44ac6c611fbd7b40716d10fe8743309"><strong>debian/patches/install_newick.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Thu, 14 Feb 2019 14:52:05 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Make sure newick is installed as well</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> Remark: This needs a hack in debian/rules - no idea how to do this more elegantly</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"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></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/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -37,7 +37,8 @@ setup(name='ragout',</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> packages=['ragout', 'ragout/assembly_graph', 'ragout/breakpoint_graph',</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> 'ragout/maf2synteny', 'ragout/overlap', 'ragout/parsers',</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> 'ragout/phylogeny', 'ragout/scaffolder', 'ragout/shared',</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;">- 'ragout/synteny_backend'],</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'ragout/synteny_backend',</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'newick'],</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> package_data={'ragout': ['LICENSE']},</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> scripts = ['bin/ragout-maf2synteny', 'bin/ragout-overlap', 'bin/ragout'],</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> cmdclass={'build': MakeBuild}</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">install_newick.patch</span></pre>
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<li id="ff985fa0cc2993a40ac1864d33d34e720e62d58c">
<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#ff985fa0cc2993a40ac1864d33d34e720e62d58c"><strong>debian/ragout-examples.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">examples</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">ragout</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#25612e51947f40549be14413f0123a318917bb1e"><strong>debian/ragout-maf2synteny.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH RAGOUT-MAF2SYNTENY "1" "February 2019" "ragout-maf2synteny 2.1.1" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">ragout-maf2synteny \- Reference-Assisted Genome Ordering UTility</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B maf2synteny</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,-o out_dir\/\fR] [\fI\,-s simpl_params\/\fR] [\fI\,-m block_sizes\/\fR] \fI\,maf_file\/\fR</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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH OPTIONS</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SS "positional arguments:"</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">maf_file</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">path to maf file</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.SS "optional arguments:"</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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.TP</span>
</pre>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">\fB\-o\fR out_dir</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">path to the output directory [default = .]</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-s\fR simpl_params path to a file with custom simplification parameters [default = not set]</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-b\fR block_sizes</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">comma\-separated list of synteny block scales [default = 5000]</span>
</pre>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.SH AUTHOR</span>
</pre>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="8927f2ecb4b13b3cc97662b867fab8b736e0e8c2">
<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#8927f2ecb4b13b3cc97662b867fab8b736e0e8c2"><strong>debian/ragout-overlap.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH RAGOUT-OVERLAP "1" "February 2019" "ragout-overlap 2.1.1" "User Commands"</span>
</pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">ragout-overlap \- Reference-Assisted Genome Ordering UTility</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B overlap</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,fasta_in dot_out min_k max_k \/\fR[\fI\,--detect-kmer\/\fR] [\fI\,--hist\/\fR]</span>
</pre>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Constructs overlap graph from input contigsand outputs it in dot format</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="1a6bd62237f1b57d96aa452beda82a2b2fa10177">
<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#1a6bd62237f1b57d96aa452beda82a2b2fa10177"><strong>debian/ragout.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH RAGOUT "1" "February 2019" "ragout 2.1.1" "User Commands"</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">ragout \- Chromosome assembly with multiple references</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B ragout</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\-h] [\-o output_dir] [\-s {sibelia,maf,hal}] [\-\-refine]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">[\-\-solid\-scaffolds] [\-\-overwrite] [\-\-repeats] [\-\-debug]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">[\-t THREADS] [\-\-version]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">recipe_file</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.SS "positional arguments:"</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">recipe_file</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">path to recipe file</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.SS "optional arguments:"</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(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="LC18" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">show this help message and exit</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-o\fR output_dir, \fB\-\-outdir\fR output_dir</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">output directory (default: ragout\-out)</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-s\fR {sibelia,maf,hal}, \fB\-\-synteny\fR {sibelia,maf,hal}</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">backend for synteny block decomposition (default:</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">sibelia)</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.TP</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-\-refine\fR</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">enable refinement with assembly graph (default: False)</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.TP</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-\-solid\-scaffolds\fR</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">do not break input sequences \- disables chimera</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">detection module (default: False)</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.TP</span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-\-overwrite\fR</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">overwrite results from the previous run (default:</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">False)</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-\-repeats\fR</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">enable repeat resolution algorithm (default: False)</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.TP</span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">\fB\-\-debug\fR</span>
</pre>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">enable debug output (default: False)</span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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45
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">number of threads for synteny backend (default: 1)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-\-version\fR</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">show program's version number and exit</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#5eaab3a6d332a70f8f7ab5b488590b063dc6f4c8"><strong>debian/ragout.install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">usr</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,22 +4,20 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># this provides:</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># DEB_SOURCE: the source package name</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM: the package's upstream version</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"># SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"># specified by <https://reproducible-builds.org/specs/source-date-epoch/></span>
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<pre style="margin: 0;"> <span id="LC7" 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="LC8" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</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">%:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh $@ --with python2 --buildsystem=pybuild</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">override_dh_auto_clean:</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> dh_auto_clean</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> if [ -L newick ] ; then rm newick ; fi</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">override_dh_auto_configure:</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> ln -s lib/newick .</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> dh_auto_configure</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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23
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">override_dh_install:</span>
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24
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> dh_install</span>
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25
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> find debian -name LICENSE -delete</span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/compare/dae78ab2ad63aa42ec0680349ffe0d6b283ef52c...b1fcb230f6b4dc696c1d4aa8111f0a625024aab6#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span>ragout</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
</pre>
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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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: navy;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-x</span></span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">ragout E.Coli/ecoli.rcp <span class="nt" style="color: navy;">--outdir</span> E.Coli/out/ <span class="nt" style="color: navy;">--refine</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">ragout H.Pylori/helicobacter.rcp <span class="nt" style="color: navy;">--outdir</span> H.Pylori/out/ <span class="nt" style="color: navy;">--refine</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">ragout S.Aureus/aureus.rcp <span class="nt" style="color: navy;">--outdir</span> S.Aureus/out/ <span class="nt" style="color: navy;">--refine</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">ragout V.Cholerae/cholerae.rcp <span class="nt" style="color: navy;">--outdir</span> V.Cholerae/out/ <span class="nt" style="color: navy;">--refine</span></span></pre>
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