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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/twopaco">Debian Med / twopaco</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/twopaco/-/commit/1265cdef2bc7c4bd262422f48adeaf7204082bd8">1265cdef</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-20T17:20:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing copyright statement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/twopaco/-/commit/bc216ede0f9b7f07abc20669e2916acc1c830606">bc216ede</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-20T17:36:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/twopaco/-/commit/a05765e920dec183104f87d26356e13ed3391a01">a05765e9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-20T17:36:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add build time test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/twopaco/-/commit/46cb5f2e37e38493ee6f8cf606823f821bfe356a">46cb5f2e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-20T18:12:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix installation, build time test and add autopkgtest
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
</span>
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
</span>
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</li>
<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<span class="new-file">
+
debian/examples
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<li class="file-stats">
<a href="#b058b28cbecf2ceba140b7dee97121994c11d7eb">
<span class="new-file">
+
debian/graphdump.1
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<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
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</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
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</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
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</li>
<li class="file-stats">
<a href="#114e0a21c02b0d54fc9bd6f87a46ac96d327a4d0">
<span class="new-file">
+
debian/twopaco.1
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/twopaco/-/compare/60ac058e17e331f89e5ed146bd9cdc5ff0a34304...46cb5f2e37e38493ee6f8cf606823f821bfe356a#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Notes</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">how</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">package</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tested</span><span class="mf" style="color: #099;">.</span></span>
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<td class="new_line diff-line-num new" 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">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
</pre>
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<td class="new_line diff-line-num new" 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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">This</span> <span class="n" style="color: #333;">package</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tested</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">running</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">provided</span> <span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
</pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="n" style="color: #333;">sh</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">unit</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">test</span></span>
</pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="n" style="color: #333;">in</span> <span class="n" style="color: #333;">order</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">confirm</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">integrity</span><span class="mf" style="color: #099;">.</span></span></pre>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/twopaco/-/compare/60ac058e17e331f89e5ed146bd9cdc5ff0a34304...46cb5f2e37e38493ee6f8cf606823f821bfe356a#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" 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">@@ -38,32 +38,44 @@ License: BSD-4-clause</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Files: src/common/ngramhashing/mersennetwister.h</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Copyright: 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> 2000 - 2003, Richard J. Wagner</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">License: BSD-3-clause</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Comment: The original code included the following notice:</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> When you use this, send an email to: matumoto@math.keio.ac.jp</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> with an appropriate reference to your work.</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"> It would be nice to CC: rjwagner@writeme.com and Cokus@math.washington.edu</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> when you write.</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">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">Copyright: 2022 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">License: BSD-3-clause</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">License: BSD-3-clause</span>
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<pre style="margin: 0;"> <span id="LC57" 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="LC58" class="line" lang="plaintext"> modification, are permitted provided that the following conditions</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> are met:</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> 1. Redistributions of source code must retain the above copyright</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> notice, this list of conditions and the following disclaimer.</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"><span class="idiff left right"> </span> 1. Redistributions of source code must retain the above copyright</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> <span class="idiff left right"> </span>notice, this list of conditions and the following disclaimer.</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> 2. Redistributions in binary form must reproduce the above copyright</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> notice, this list of conditions and the following disclaimer in</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> the documentation and/or other materials provided with the</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> distribution.</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> 2. Redistributions in binary form must reproduce the above copyright</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> notice, this list of conditions and the following disclaimer in the</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> documentation and/or other materials provided with the distribution.</span>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> 3. <span class="idiff left">Neither t</span>he name of <span class="idiff right">the copyright holder nor the names of its</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> <span class="idiff left right">contributors may be used to endorse or promote products derived</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> <span class="idiff left right">from this software without specific prior written</span> permission.</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"><span class="idiff left"> </span> 3. <span class="idiff">T</span>he name<span class="idiff">s</span> of <span class="idiff right">its contributors may not be used to endorse or promote </span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> <span class="idiff left right"> products derived from this software without specific prior written </span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> <span class="idiff left right"> </span> permission.</span>
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59
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"> "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT</span>
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62
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"><span class="idiff left right"> HOLDER OR</span> CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"><span class="idiff left right"> SPECIAL,</span> EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"><span class="idiff left right"> TO,</span> PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> A PARTICULAR PURPOSE ARE DISCLAIMED. <span class="idiff left"> </span>IN NO EVENT SHALL THE COPYRIGHT<span class="idiff right"> OWNER OR</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,<span class="idiff left right"> SPECIAL,</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED<span class="idiff left right"> TO,</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR</span>
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67
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF</span>
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68
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"> LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING</span>
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69
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"> NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS</span>
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<a href="https://salsa.debian.org/med-team/twopaco/-/compare/60ac058e17e331f89e5ed146bd9cdc5ff0a34304...46cb5f2e37e38493ee6f8cf606823f821bfe356a#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>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-x</span> /usr/bin/help2man <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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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"E: Missing /usr/bin/help2man, please install it from the cognate package."</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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<td class="new_line diff-line-num new" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$PROGNAME</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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<td class="new_line diff-line-num new" 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"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nv" style="color: #008080;">HELPOPTION</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">--help</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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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="s2" style="color: #d14;">"PROGNAME: '</span><span class="nv" style="color: #008080;">$PROGNAME</span><span class="s2" style="color: #d14;">'"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"NAME: '</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">'"</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"VERSION: '</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">'"</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"MANDIR: '</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">'"</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"HELPOPTION: '</span><span class="nv" style="color: #008080;">$HELPOPTION</span><span class="s2" 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>
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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;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"></span>
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39
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<pre style="margin: 0;">+<span id="LC39" 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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40
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<pre style="margin: 0;">+<span id="LC40" 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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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PROGNAME</span><span class="k" style="font-weight: 600;">}</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$HELPOPTION</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>graphdump</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$HELPOPTION</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output in '</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="sh" style="color: #d14;">/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span><span class="sh" style="color: #d14;">.1'.</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="sh" style="color: #d14;">To inspect it, try 'nroff -man </span><span class="nv" style="color: #008080;">$MANDIR</span><span class="sh" style="color: #d14;">/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span><span class="sh" style="color: #d14;">.1'.</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="sh" style="color: #d14;">If very unhappy, try passing the HELPOPTION as an environment variable.</span></span>
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<pre style="margin: 0;">+<span id="LC59" 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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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/med-team/twopaco/-/compare/60ac058e17e331f89e5ed146bd9cdc5ff0a34304...46cb5f2e37e38493ee6f8cf606823f821bfe356a#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">example/*</span></pre>
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<a href="https://salsa.debian.org/med-team/twopaco/-/compare/60ac058e17e331f89e5ed146bd9cdc5ff0a34304...46cb5f2e37e38493ee6f8cf606823f821bfe356a#b058b28cbecf2ceba140b7dee97121994c11d7eb"><strong>debian/graphdump.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 1.49.1.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH GRAPHDUMP "1" "February 2022" "graphdump 0.9.4" "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">graphdump \- build the compacted de Bruijn graph from many complete genomes</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">USAGE:</span>
</pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.TP</span>
</pre>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">graphdump</span>
</pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">\fB\-k\fR <integer> [\-s <>] ... \fB\-f\fR <seq|group|dot|gfa1|gfa2|fasta></span>
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<td class="new_line diff-line-num new" 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="plaintext">[\-\-prefix] [\-\-] [\-\-version] [\-h] <file name></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="old_line diff-line-num new" 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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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Where:</span>
</pre>
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<td class="new_line diff-line-num new" 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="plaintext">.HP</span>
</pre>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-k\fR <integer>, \fB\-\-kvalue\fR <integer></span>
</pre>
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<td class="new_line diff-line-num new" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">(required)</span>
</pre>
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<td class="old_line diff-line-num new" 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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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Value of k</span>
</pre>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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="plaintext">\fB\-s\fR <>, \fB\-\-seqfile\fR <></span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">(accepted multiple times)</span>
</pre>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="old_line diff-line-num new" 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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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">sequences file name</span>
</pre>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-f\fR <seq|group|dot|gfa1|gfa2|fasta>, \fB\-\-format\fR <seq|group|dot|gfa1|gfa2</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">|fasta></span>
</pre>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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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="LC28" class="line" lang="plaintext">(required)</span>
</pre>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Output format</span>
</pre>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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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="LC30" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-\-prefix\fR</span>
</pre>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Add a prefix to segments in GFA (in case if you have genomes with</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">identical FASTA headers)</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.HP</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-\-\fR, \fB\-\-ignore_rest\fR</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.IP</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Ignores the rest of the labeled arguments following this flag.</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.HP</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-\-version\fR</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.IP</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Displays version information and exits.</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Displays usage information and exits.</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"><file name></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">(required)</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">input file name</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">This utility converts the binary output of TwoPaCo to another format</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/twopaco/-/compare/60ac058e17e331f89e5ed146bd9cdc5ff0a34304...46cb5f2e37e38493ee6f8cf606823f821bfe356a#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/twopaco/-/compare/60ac058e17e331f89e5ed146bd9cdc5ff0a34304...46cb5f2e37e38493ee6f8cf606823f821bfe356a#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">@@ -11,7 +11,17 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> dh $@ --sourcedir=src</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> obj-*/graphconstructor/twopaco --test -f 34 example/example.fa</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> obj-*/graphconstructor/twopaco -f 20 -k 11 example/example.fa -o example/example.dbg</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> obj-*/graphdump/graphdump -f dot example/example.dbg -k 11 > example/example.dot</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">override_dh_installexamples:</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> dh_installexamples --sourcedir=$(CURDIR)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">override_dh_installman:</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> dh_installman --sourcedir=$(CURDIR)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"># For some reason debian/not-installed does not work</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">override_dh_missing:</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> dh_missing --list-missing</span></pre>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/twopaco/-/compare/60ac058e17e331f89e5ed146bd9cdc5ff0a34304...46cb5f2e37e38493ee6f8cf606823f821bfe356a#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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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/twopaco/-/compare/60ac058e17e331f89e5ed146bd9cdc5ff0a34304...46cb5f2e37e38493ee6f8cf606823f821bfe356a#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>twopaco</span>
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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="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">twopaco <span class="nt" style="color: #000080;">--test</span> <span class="nt" style="color: #000080;">-f</span> 34 example.fa</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">twopaco <span class="nt" style="color: #000080;">-f</span> 20 <span class="nt" style="color: #000080;">-k</span> 11 example.fa <span class="nt" style="color: #000080;">-o</span> example.dbg</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">graphdump <span class="nt" style="color: #000080;">-f</span> dot example.dbg <span class="nt" style="color: #000080;">-k</span> 11 <span class="o" style="font-weight: 600;">></span> example.dot</span></pre>
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<a href="https://salsa.debian.org/med-team/twopaco/-/compare/60ac058e17e331f89e5ed146bd9cdc5ff0a34304...46cb5f2e37e38493ee6f8cf606823f821bfe356a#114e0a21c02b0d54fc9bd6f87a46ac96d327a4d0"><strong>debian/twopaco.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 1.49.1.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH TWOPACO "1" "February 2022" "twopaco 0.9.4" "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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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">twopaco \- build the compacted de Bruijn graph from many complete genomes</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">USAGE:</span>
</pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.TP</span>
</pre>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">twopaco</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">{\-f <integer>|\-\-filtermemory <float>} [\-o <file name>] [\-\-test]</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">[\-\-tmpdir <directory name>] [\-a <integer>] [\-t <integer>] [\-r</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><integer>] [\-q <integer>] [\-k <oddc>] [\-\-] [\-\-version] [\-h]</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"><fasta files with genomes> ...</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.PP</span>
</pre>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Where:</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.HP</span>
</pre>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-f\fR <integer>, \fB\-\-filtersize\fR <integer></span>
</pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">(OR required)</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Size of the filter</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.HP</span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-\-\fR OR \fB\-\-\fR</span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.HP</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-\-filtermemory\fR <float></span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">(OR required)</span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Memory in GBs allocated for the filter</span>
</pre>
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<td class="old_line diff-line-num new" 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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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="old_line diff-line-num new" 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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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-o\fR <file name>, \fB\-\-outfile\fR <file name></span>
</pre>
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<td class="old_line diff-line-num new" 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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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="old_line diff-line-num new" 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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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Output file name prefix</span>
</pre>
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<td class="old_line diff-line-num new" 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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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.HP</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-\-test\fR</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.IP</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Run tests</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.HP</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-\-tmpdir\fR <directory name></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.IP</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Temporary directory name</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.HP</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-a\fR <integer>, \fB\-\-abundance\fR <integer></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.IP</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Vertex abundance threshold</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.HP</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-t\fR <integer>, \fB\-\-threads\fR <integer></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.IP</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Number of worker threads</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.HP</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-r\fR <integer>, \fB\-\-rounds\fR <integer></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.IP</span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">Number of computation rounds</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.HP</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">\fB\-q\fR <integer>, \fB\-\-hashfnumber\fR <integer></span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.IP</span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Number of hash functions</span>
</pre>
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<td class="old_line diff-line-num new" 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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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.HP</span>
</pre>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">\fB\-k\fR <oddc>, \fB\-\-kvalue\fR <oddc></span>
</pre>
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<td class="old_line diff-line-num new" 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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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">.IP</span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">Value of k</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">.HP</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">\fB\-\-\fR, \fB\-\-ignore_rest\fR</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">.IP</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">Ignores the rest of the labeled arguments following this flag.</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">.HP</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">\fB\-\-version\fR</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.IP</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">Displays version information and exits.</span>
</pre>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.HP</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">.IP</span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">Displays usage information and exits.</span>
</pre>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">.TP</span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"><fasta files with genomes></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">(accepted multiple times)</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.TP</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">(required)</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">FASTA file(s) with nucleotide sequences.</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">.IP</span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">Program for construction of the condensed de Bruijn graph from complete</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">genomes</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">.SH AUTHOR</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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