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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/centrifuge">Debian Med / centrifuge</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/centrifuge/-/commit/be375c33b68f4038a233aa0d7ae41618904eafeb">be375c33</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-12T07:43:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix watchfile to detect new versions on github
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/centrifuge/-/commit/88a3227c89f13415a9bc32abf57ac911f504acf1">88a3227c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-12T07:44:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/centrifuge/-/commit/a827640ff8ccd864bfbd8bf4c80539f2b39f1ff2">a827640f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-12T08:43:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/centrifuge/-/commit/3fc0cffa987f45271a2fe78c0c75fb64b4c9f533">3fc0cffa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-12T08:45:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
debian/createmanpages
</a>
</li>
<li class="file-stats">
<a href="#9354eaf9370ebc0bfec058f4b440a1bd871b20fc">
debian/mans/centrifuge-build.1
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<li class="file-stats">
<a href="#d4ff6f423a82a329ab4d1eae9ab5a45157f103cd">
debian/mans/centrifuge-compress.1
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<li class="file-stats">
<a href="#cbe75068a6247a44b2fc7e08781f807b9578b80e">
debian/mans/centrifuge-download.1
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<li class="file-stats">
<a href="#36ba1a3af9a6a5a117a52dbe78302409e0bb5b50">
debian/mans/centrifuge-inspect.1
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<li class="file-stats">
<a href="#602ac365059996ea238be01bce2e329ed1f73e4b">
debian/mans/centrifuge.1
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/centrifuge/-/compare/4c6b9dd49d6b3cf34faa5245c05449dcfd75b877...3fc0cffa987f45271a2fe78c0c75fb64b4c9f533#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">centrifuge (1.0.3-9) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github</span>
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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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Fix manpages</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 12 Oct 2021 08:43:55 +0200</span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">centrifuge (1.0.3-8) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num" data-linenumber="11" 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">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> [ Helmut Grohne ]</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/centrifuge/-/compare/4c6b9dd49d6b3cf34faa5245c05449dcfd75b877...3fc0cffa987f45271a2fe78c0c75fb64b4c9f533#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-sequence-python3,</span>
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> jellyfish</span>
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<td class="new_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5</span>.0</span>
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<td class="old_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">
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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="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6</span>.0</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/centrifuge</span>
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<td class="old_line diff-line-num" data-linenumber="12" 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">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/centrifuge.git</span>
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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: https://ccb.jhu.edu/software/centrifuge/</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,31 +11,32 @@ can be used for any other usage of the program.</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>centrifuge</span>
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<pre style="margin: 0;"> <span id="LC12" 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;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'rapid and memory-efficient system for classification of DNA sequences'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC14" 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="LC14" 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;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="idiff left right">/usr/bin/</span><span class="k" style="font-weight: 600;">${</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="LC15" 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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>centrifuge-build</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'building index on all complete bacterial and viral genomes'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="idiff left right">/usr/bin/</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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$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="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>centrifuge-compress</span>
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<pre style="margin: 0;"> <span id="LC24" 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="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'genome compression in the database construction'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC26" 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="LC26" 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;">$VERSION</span><span class="s2" style="color: #d14;">"</span> /usr/bin/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/USAGE: perl centrifuge\\-compress.pl/centrifuge\-compress/'</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="LC28" 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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>centrifuge-download</span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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31
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'centrifuge helper to download databases'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="idiff left right">/usr/bin/</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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$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="LC35" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>centrifuge-inspect</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--<span class="idiff left right">no-</span>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;">" -h"</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">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--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;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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37
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'inspecting the centrifuge index'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC38" 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="LC39" 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;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="idiff left right">/usr/bin/</span><span class="k" style="font-weight: 600;">${</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="LC40" 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="LC41" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC42" 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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<a href="https://salsa.debian.org/med-team/centrifuge/-/compare/4c6b9dd49d6b3cf34faa5245c05449dcfd75b877...3fc0cffa987f45271a2fe78c0c75fb64b4c9f533#9354eaf9370ebc0bfec058f4b440a1bd871b20fc"><strong>debian/mans/centrifuge-build.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 1.4<span class="idiff left right">7.5</span>.</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH CENTRIFUGE-BUILD "1" "<span class="idiff left">Decem</span>ber 201<span class="idiff">7</span>" "centrifuge-build 1.0.3<span class="idiff right">~beta</span>" "User Commands"</span>
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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 1.4<span class="idiff left right">8.1</span>.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH CENTRIFUGE-BUILD "1" "<span class="idiff left">Octo</span>ber 20<span class="idiff right">2</span>1" "centrifuge-build 1.0.3" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">centrifuge-build \- building index on all complete bacterial and viral genomes</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B centrifuge-build</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR]\fI\,* --conversion-table <table file> --taxonomy-tree <taxonomy tree file> <reference_in> <cf_index_base>\/\fR</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">.SS "Traceback (most recent call last):"</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">File "./centrifuge\-build", line 79, in <module></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">main()</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">File "./centrifuge\-build", line 76, in main</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">os.execv(build_bin_spec, argv)</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">OSError: [Errno 2] No such file or directory</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Centrifuge version 1.0.3\-beta by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">reference_in</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">comma\-separated list of files with ref sequences</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">centrifuge_index_base</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">write cf data to files with this dir/basename</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.SH OPTIONS</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-c\fR</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">reference sequences given on cmd line (as</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"><reference_in>)</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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">\fB\-\-large\-index\fR</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">force generated index to be 'large', even if ref</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">has fewer than 4 billion nucleotides</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-a\fR/\-\-noauto</span>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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">disable automatic \fB\-p\fR/\-\-bmax/\-\-dcv memory\-fitting</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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">\fB\-\-bmax\fR <int></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">max bucket sz for blockwise suffix\-array builder</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-\-bmaxdivn\fR <int></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">max bucket sz as divisor of ref len (default: 4)</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-\-dcv\fR <int></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">diff\-cover period for blockwise (default: 1024)</span>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.TP</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-\-nodc\fR</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">disable diff\-cover (algorithm becomes quadratic)</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.TP</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-r\fR/\-\-noref</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">don't build .3/.4.bt2 (packed reference) portion</span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-3\fR/\-\-justref</span>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">just build .3/.4.bt2 (packed reference) portion</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-o\fR/\-\-offrate <int></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">SA is sampled every 2^offRate BWT chars (default: 5)</span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">\fB\-t\fR/\-\-ftabchars <int></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"># of chars consumed in initial lookup (default: 10)</span>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">\fB\-\-conversion\-table\fR <file name></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
54
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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="LC54" class="line" lang="plaintext">a table that converts any id to a taxonomy id</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
56
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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="LC56" class="line" lang="plaintext">\fB\-\-taxonomy\-tree\fR</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
57
</td>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"><file name> taxonomy tree</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.TP</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">\fB\-\-name\-table\fR</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"><file name> names corresponding to taxonomic IDs</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">\fB\-\-size\-table\fR</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
</td>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"><file name> table of contig (or genome) sizes</span>
</pre>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">.TP</span>
</pre>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">\fB\-\-seed\fR <int></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">seed for random number generator</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.TP</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">\fB\-q\fR/\-\-quiet</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">verbose output (for debugging)</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">\fB\-p\fR/\-\-threads <int></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">number of alignment threads to launch (1)</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">\fB\-\-kmer\-count\fR <int></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">k size for counting the number of distinct k\-mer</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">\fB\-h\fR/\-\-help</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">print detailed description of tool and its options</span>
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">\fB\-\-usage\fR</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">print this usage message</span>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">\fB\-\-version\fR</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">print version information and quit</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
17
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext">.SH AUTHOR</span>
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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<td class="new_line diff-line-num" data-linenumber="86" 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">
86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="d4ff6f423a82a329ab4d1eae9ab5a45157f103cd">
<a href="https://salsa.debian.org/med-team/centrifuge/-/compare/4c6b9dd49d6b3cf34faa5245c05449dcfd75b877...3fc0cffa987f45271a2fe78c0c75fb64b4c9f533#d4ff6f423a82a329ab4d1eae9ab5a45157f103cd"><strong>debian/mans/centrifuge-compress.1</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.4<span class="idiff left right">7.5</span>.</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH CENTRIFUGE-COMPRESS "1" "<span class="idiff left">Decem</span>ber 201<span class="idiff">7</span>" "centrifuge-compress 1.0.3<span class="idiff right">~beta</span>" "User Commands"</span>
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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 1.4<span class="idiff left right">8.1</span>.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH CENTRIFUGE-COMPRESS "1" "<span class="idiff left">Octo</span>ber 20<span class="idiff right">2</span>1" "centrifuge-compress 1.0.3" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">centrifuge-compress \- genome compression in the database construction</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"><span class="idiff left">USAGE: perl </span>centrifuge<span class="idiff">\</span>-compress<span class="idiff right">.pl</span> path_to_download_files path_to_taxnonomy [\-map header_to_taxid_map \fB\-o\fR compressed \fB\-noCompress\fR \fB\-t\fR 1 \fB\-maxG\fR 50000000 \fB\-noDustmasker]\fR</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">centrifuge-compress path_to_download_files path_to_taxnonomy [\-map header_to_taxid_map \fB\-o\fR compressed \fB\-noCompress\fR \fB\-t\fR 1 \fB\-maxG\fR 50000000 \fB\-noDustmasker]\fR</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/centrifuge/-/compare/4c6b9dd49d6b3cf34faa5245c05449dcfd75b877...3fc0cffa987f45271a2fe78c0c75fb64b4c9f533#cbe75068a6247a44b2fc7e08781f807b9578b80e"><strong>debian/mans/centrifuge-download.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 1.4<span class="idiff left right">7.5</span>.</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH CENTRIFUGE-DOWNLOAD "1" "<span class="idiff left">Decem</span>ber 201<span class="idiff">7</span>" "centrifuge-download 1.0.3<span class="idiff right">~beta</span>" "User Commands"</span>
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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 1.4<span class="idiff left right">8.1</span>.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH CENTRIFUGE-DOWNLOAD "1" "<span class="idiff left">Octo</span>ber 20<span class="idiff right">2</span>1" "centrifuge-download 1.0.3" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">centrifuge-download \- centrifuge helper to download databases</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +27,7 @@ Number of processes when downloading (uses xargs). Default: '1'</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">What domain to download. One or more of bacteria, viral, archaea, fungi, protozoa, invertebrate, plant, vertebrate_mammalian, vertebrate_other (comma separated).</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">\fB\-a\fR <assembly level></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">Only download genomes with the specified assembly level. Default: 'Complete Genome'.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Only download genomes with the specified assembly level. Default: 'Complete Genome'.<span class="idiff left right"> Use 'Any' for any assembly level.</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">\fB\-c\fR <refseq category></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Only download genomes in the specified refseq category. Default: any.</span>
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<a href="https://salsa.debian.org/med-team/centrifuge/-/compare/4c6b9dd49d6b3cf34faa5245c05449dcfd75b877...3fc0cffa987f45271a2fe78c0c75fb64b4c9f533#36ba1a3af9a6a5a117a52dbe78302409e0bb5b50"><strong>debian/mans/centrifuge-inspect.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 1.4<span class="idiff left right">7.5</span>.</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH CENTRIFUGE-INSPECT "1" "<span class="idiff left">Decem</span>ber 201<span class="idiff">7</span>" "centrifuge-inspect 1.0.3<span class="idiff right">~beta</span>" "User Commands"</span>
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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 1.4<span class="idiff left right">8.1</span>.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH CENTRIFUGE-INSPECT "1" "<span class="idiff left">Octo</span>ber 20<span class="idiff right">2</span>1" "centrifuge-inspect 1.0.3" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">centrifuge-inspect \- inspecting the centrifuge index</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B centrifuge-inspect</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR]\fI\,* <cf_base>\/\fR</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">.SS "Traceback (most recent call last):"</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Centrifuge version 1.0.3\-beta by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><cf_base></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">cf filename minus trailing .1.cf/.2.cf/.3.cf</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">File "./centrifuge\-inspect", line 55, in <module></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">main()</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">File "./centrifuge\-inspect", line 51, in main</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">os.execv(inspect_bin_spec, arguments)</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">OSError: [Errno 2] No such file or directory</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">By default, prints FASTA records of the indexed nucleotide sequences to</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">standard out. With \fB\-n\fR, just prints names. With \fB\-s\fR, just prints a summary of</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">the index parameters and sequences. With \fB\-e\fR, preserves colors if applicable.</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.SH OPTIONS</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-\-large\-index\fR</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">force inspection of the 'large' index, even if a</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\&'small' one is present.</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-a\fR/\-\-across <int></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Number of characters across in FASTA output (default: 60)</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-n\fR/\-\-names</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Print reference sequence names only</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-s\fR/\-\-summary</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Print summary incl. ref names, lengths, index properties</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-e\fR/\-\-bt2\-ref</span>
</pre>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Reconstruct reference from .cf (slow, preserves colors)</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.HP</span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-\-conversion\-table\fR Print conversion table</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(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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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-\-taxonomy\-tree\fR</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Print taxonomy tree</span>
</pre>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.TP</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-\-name\-table\fR</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Print names corresponding to taxonomic IDs</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.TP</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">\fB\-\-size\-table\fR</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Print the lengths of the sequences belonging to the same taxonomic ID</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.TP</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">\fB\-v\fR/\-\-verbose</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Verbose output (for debugging)</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">\fB\-h\fR/\-\-help</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">print detailed description of tool and its options</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">\fB\-\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">print this usage message</span>
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17
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">.SH AUTHOR</span>
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18
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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 can be used for any other usage of the program.</span></pre>
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<li id="602ac365059996ea238be01bce2e329ed1f73e4b">
<a href="https://salsa.debian.org/med-team/centrifuge/-/compare/4c6b9dd49d6b3cf34faa5245c05449dcfd75b877...3fc0cffa987f45271a2fe78c0c75fb64b4c9f533#602ac365059996ea238be01bce2e329ed1f73e4b"><strong>debian/mans/centrifuge.1</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.4<span class="idiff left right">7.5</span>.</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH CENTRIFUGE "1" "<span class="idiff left">Decem</span>ber 201<span class="idiff">7</span>" "centrifuge 1.0.3<span class="idiff right">~beta</span>" "User Commands"</span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.4<span class="idiff left right">8.1</span>.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH CENTRIFUGE "1" "<span class="idiff left">Octo</span>ber 20<span class="idiff right">2</span>1" "centrifuge 1.0.3" "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">centrifuge \- rapid and memory-efficient system for classification of DNA sequences</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">(ERR): Expected centrifuge to be in same directory with centrifuge\-class:</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">/home/andreas/debian\-maintain/alioth/debian\-med_git/0_prospective/centrifuge/</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Exiting now ...</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Centrifuge version 1.0.3\-beta by the Centrifuge developer team (centrifuge.metagenomics@gmail.com)</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Usage:</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.IP</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">centrifuge [options]* \fB\-x\fR <cf\-idx> {\-1 <m1> \fB\-2\fR <m2> | \fB\-U\fR <r>} [\-S <filename>] [\-\-report\-file <report>]</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
</pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><cf\-idx></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Index filename prefix (minus trailing .X.cf).</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"><m1></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Files with #1 mates, paired with files in <m2>.</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).</span>
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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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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"><m2></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Files with #2 mates, paired with files in <m1>.</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"><r></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Files with unpaired reads.</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"><filename></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">File for classification output (default: stdout)</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"><report></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">File for tabular report output (default: centrifuge_report.tsv)</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.IP</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"><m1>, <m2>, <r> can be comma\-separated lists (no whitespace) and can be</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">specified many times. E.g. '\-U file1.fq,file2.fq \fB\-U\fR file3.fq'.</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.PP</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Options (defaults in parentheses):</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.IP</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Input:</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-q\fR</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">query input files are FASTQ .fq/.fastq (default)</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.TP</span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">\fB\-\-qseq\fR</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">query input files are in Illumina's qseq format</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.TP</span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">\fB\-f\fR</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">query input files are (multi\-)FASTA .fa/.mfa</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-r\fR</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">query input files are raw one\-sequence\-per\-line</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.TP</span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">\fB\-c\fR</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"><m1>, <m2>, <r> are sequences themselves, not files</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">\fB\-s\fR/\-\-skip <int></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">skip the first <int> reads/pairs in the input (none)</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">\fB\-u\fR/\-\-upto <int></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">stop after first <int> reads/pairs (no limit)</span>
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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">.TP</span>
</pre>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">\fB\-5\fR/\-\-trim5 <int></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">trim <int> bases from 5'/left end of reads (0)</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">\fB\-3\fR/\-\-trim3 <int></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">trim <int> bases from 3'/right end of reads (0)</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">\fB\-\-phred33\fR</span>
</pre>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">qualities are Phred+33 (default)</span>
</pre>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">\fB\-\-phred64\fR</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">qualities are Phred+64</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">\fB\-\-int\-quals\fR</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">qualities encoded as space\-delimited integers</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">\fB\-\-ignore\-quals\fR</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">treat all quality values as 30 on Phred scale (off)</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">\fB\-\-nofw\fR</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">do not align forward (original) version of read (off)</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">\fB\-\-norc\fR</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">do not align reverse\-complement version of read (off)</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">.SS "Classification:"</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">.TP</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">\fB\-\-min\-hitlen\fR <int></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">minimum length of partial hits (default 22, must be greater than 15)</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.TP</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">\fB\-\-min\-totallen\fR <int></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">minimum summed length of partial hits per read (default 0)</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">.HP</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">\fB\-\-host\-taxids\fR <taxids> comma\-separated list of taxonomic IDs that will be preferred in classification</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">.HP</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">\fB\-\-exclude\-taxids\fR <taxids> comma\-separated list of taxonomic IDs that will be excluded in classification</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">.IP</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">Output:</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">.TP</span>
</pre>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">\fB\-\-out\-fmt\fR <str></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">define output format, either 'tab' or 'sam' (tab)</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">.TP</span>
</pre>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">\fB\-\-tab\-fmt\-cols\fR <str></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">columns in tabular format, comma separated</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">default: readID,seqID,taxID,score,2ndBestScore,hitLength,queryLength,numMatches</span>
</pre>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">.TP</span>
</pre>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">\fB\-t\fR/\-\-time</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">print wall\-clock time taken by search phases</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">.TP</span>
</pre>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">\fB\-\-un\fR <path></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">write unpaired reads that didn't align to <path></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">.TP</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">\fB\-\-al\fR <path></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">write unpaired reads that aligned at least once to <path></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">.TP</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">\fB\-\-un\-conc\fR <path></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">write pairs that didn't align concordantly to <path></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">.TP</span>
</pre>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">\fB\-\-al\-conc\fR <path></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">write pairs that aligned concordantly at least once to <path></span>
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">.IP</span>
</pre>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">(Note: for \fB\-\-un\fR, \fB\-\-al\fR, \fB\-\-un\-conc\fR, or \fB\-\-al\-conc\fR, add '\-gz' to the option name, e.g.</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">\fB\-\-un\-gz\fR <path>, to gzip compress output, or add '\-bz2' to bzip2 compress output.)</span>
</pre>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">\fB\-\-quiet\fR print nothing to stderr except serious errors</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">\fB\-\-met\-file\fR <path> send metrics to file at <path> (off)</span>
</pre>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">\fB\-\-met\-stderr\fR send metrics to stderr (off)</span>
</pre>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">\fB\-\-met\fR <int> report internal counters & metrics every <int> secs (1)</span>
</pre>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">.IP</span>
</pre>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">Performance:</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">\fB\-o\fR/\-\-offrate <int> override offrate of index; must be >= index's offrate</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">.HP</span>
</pre>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">\fB\-p\fR/\-\-threads <int> number of alignment threads to launch (1)</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">\fB\-\-mm\fR</span>
</pre>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">use memory\-mapped I/O for index; many instances can share</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">.IP</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">Other:</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">.TP</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">\fB\-\-qc\-filter\fR</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">filter out reads that are bad according to QSEQ filter</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">.TP</span>
</pre>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">\fB\-\-seed\fR <int></span>
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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">seed for random number generator (0)</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">.HP</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">\fB\-\-non\-deterministic\fR seed rand. gen. arbitrarily instead of using read attributes</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">.TP</span>
</pre>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">\fB\-\-version\fR</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">print version information and quit</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">.TP</span>
</pre>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">\fB\-h\fR/\-\-help</span>
</pre>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">print this usage message</span>
</pre>
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9
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext">.SH AUTHOR</span>
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10
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<td class="new_line diff-line-num" data-linenumber="151" 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">
151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/centrifuge/-/compare/4c6b9dd49d6b3cf34faa5245c05449dcfd75b877...3fc0cffa987f45271a2fe78c0c75fb64b4c9f533#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">https://github.com//infphilo/centrifuge/releases .*/<span class="idiff left right">archive/</span>v?(\d[.\d]+)@ARCHIVE_EXT@</span></pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">https://github.com//infphilo/centrifuge/releases .*/v?(\d[.\d]+)@ARCHIVE_EXT@</span></pre>
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