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GitLab

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<h3>

Nilesh Patra pushed to branch master

at <a href="https://salsa.debian.org/med-team/proteinortho">Debian Med / proteinortho</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/15a2175122ae81d17757bb008f345bdeb272be94">15a21751</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-02-01T15:54:33+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add myself to uploaders

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/941908d6f5d27c5297836775c10a3597286ff2c8">941908d6</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-02-01T15:55:01+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/6db4d97b2bd51ad57b2810a7aa0eb7f89840016d">6db4d97b</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-02-01T15:55:02+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 6.0.28+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/5fc3b4177483e29843ec9bab005750f853673f1b">5fc3b417</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-02-01T15:55:04+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/6.0.28+dfsg'

Update to upstream version '6.0.28+dfsg'

with Debian dir 023382c0d1836d10c67f4847eb56f3e18d95becc</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/1486e86627af5db48ee03731c56323b6e19a05ee">1486e866</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-02-01T15:55:28+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>7 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">

CHANGELOG

</a>

</li>

<li class="file-stats">

<a href="#ff6936350384213d6f693f4d604134188ce088c8">

CHANGEUID

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#c9e37a96ac72f9ef076d7a41a57470524d63b36e">

proteinortho6.pl

</a>

</li>

<li class="file-stats">

<a href="#ba368ee46e511166051985e745eaa37aea49d150">

src/proteinortho_clustering.cpp

</a>

</li>

<li class="file-stats">

<a href="#3439148ea7017354388f7c55043cc84986c1c394">

src/proteinortho_grab_proteins.pl

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/9e6c42c356a281fb5b32f95587dd63adfe0178e4...1486e86627af5db48ee03731c56323b6e19a05ee#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong>CHANGELOG</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="287" 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="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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287

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="plaintext">            proteinortho.summary will be omitted if -nograph is set (there is no graph to generate a summary from)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="plaintext">    10. Jan (5379)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="289" 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="LC289" class="line" lang="plaintext">            last update introduced a bug that removes the *.blast-graph if --step=3 is used</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="290" 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="LC290" class="line" lang="plaintext">    29. Jan (5399)</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="291" 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="LC291" class="line" lang="plaintext">            fixed a bug (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/44) involving the --isoform=trinity option (search pattern was too strict), thanks to Sasha Sh !</span></pre>

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<tr class="line_holder new-nonewline" id="" style="line-height: 1.6;">

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<td class="new_line diff-line-num" 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">\ No newline at end of file</td>

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</li>

<li id="ff6936350384213d6f693f4d604134188ce088c8">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/9e6c42c356a281fb5b32f95587dd63adfe0178e4...1486e86627af5db48ee03731c56323b6e19a05ee#ff6936350384213d6f693f4d604134188ce088c8"><strong>CHANGEUID</strong></a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">53<span class="idiff left right">7</span>9</span></pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">53<span class="idiff left right">9</span>9</span></pre>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/9e6c42c356a281fb5b32f95587dd63adfe0178e4...1486e86627af5db48ee03731c56323b6e19a05ee#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">proteinortho (6.0.28+dfsg-1) unstable; urgency=medium</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com>  Mon, 01 Feb 2021 15:55:28 +0530</span>

</pre>

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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">proteinortho (6.0.27+dfsg-1) unstable; urgency=medium</span>

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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">  * Team upload.</span>

</pre>

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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/9e6c42c356a281fb5b32f95587dd63adfe0178e4...1486e86627af5db48ee03731c56323b6e19a05ee#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: proteinortho</span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org><span class="idiff left right">, Nilesh Patra <npatra974@gmail.com></span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>

</pre>

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</li>

<li id="c9e37a96ac72f9ef076d7a41a57470524d63b36e">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/9e6c42c356a281fb5b32f95587dd63adfe0178e4...1486e86627af5db48ee03731c56323b6e19a05ee#c9e37a96ac72f9ef076d7a41a57470524d63b36e"><strong>proteinortho6.pl</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -464,7 +464,7 @@ use POSIX;</td>

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Variables</span></span>

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<pre style="margin: 0;"> <span id="LC466" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

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<pre style="margin: 0;">-<span id="LC467" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.2<span class="idiff left right">7</span></span><span class="p">";</span></span>

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.2<span class="idiff left right">8</span></span><span class="p">";</span></span>

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<pre style="margin: 0;"> <span id="LC468" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span>    <span class="c1" style="color: #998; font-style: italic;"># 0/1/2/3 -> do all / only apply step 1 / only apply step 2 / only apply step 3</span></span>

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<td class="diff-line-num new_line" data-linenumber="469" 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="LC469" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1   -> don't / be verbose</span></span>

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<td class="diff-line-num new_line" data-linenumber="470" 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="LC470" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span>   <span class="c1" style="color: #998; font-style: italic;"># 0/1   -> don't / show debug data</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -500,6 +500,7 @@ our $doxml = 0;</td>

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<pre style="margin: 0;"> <span id="LC500" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="501" 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="LC501" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$tmp_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>

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<td class="diff-line-num old_line" data-linenumber="502" 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="LC502" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$useMcl</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC503" class="line" lang="perl"><span class="vg" style="color: #008080;">$|</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">#autoflush</span></span>

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<td class="diff-line-num new_line" data-linenumber="504" 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="LC504" class="line" lang="perl"></span>

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<td class="diff-line-num new_line" data-linenumber="505" 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="LC505" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Internal</span></span>

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<td class="diff-line-num new_line" data-linenumber="506" 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="LC506" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$blastversion</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">unknown</span><span class="p">";</span>  <span class="c1" style="color: #998; font-style: italic;"># Auto-detected blastmode version</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="641" 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="642" 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">@@ -641,7 +642,7 @@ if($selfblast){$checkblast=1;}</td>

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<pre style="margin: 0;"> <span id="LC642" class="line" lang="perl"></span>

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<td class="diff-line-num new_line" data-linenumber="643" 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="LC643" class="line" lang="perl"><span class="nv" style="color: #008080;">$po_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">&get_po_path</span><span class="p">();</span>    <span class="c1" style="color: #998; font-style: italic;"># Determine local path</span></span>

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<td class="diff-line-num new_line" data-linenumber="644" 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="LC644" class="line" lang="perl"></span>

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<td class="diff-line-num new_line old" data-linenumber="645" 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="LC644" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$nucleotideAlphabet</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">ACGT<span class="idiff left">URYSWKMBDHVNXacgturyswkmbdhvnx</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">.</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">-</span></span><span class="p"><span class="idiff right">";</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="645" 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="LC645" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$nucleotideAlphabet</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">ACGT<span class="idiff left">Nacgtn</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">.</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">-</span></span><span class="p"><span class="idiff">";</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">#ACGTURYSWKMBDHVNXacgturyswkmbdhvnx</span></span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="646" 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="LC646" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$aminoAlphabet</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">XOUBZACDEFGHIKLMNPQRSTVWYxoubzacdefghiklmnpqrstvwy</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">*</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">-</span><span class="p">";</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC647" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">%autoblast_fileis</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="648" 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="LC648" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$allowedAlphabet</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1008" 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="1009" 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">@@ -1008,7 +1009,8 @@ sub cluster {</td>

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1008

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<td class="diff-line-num new_line" data-linenumber="1009" 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">

1009

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<pre style="margin: 0;"> <span id="LC1009" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cluster_verbose_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1009" 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">

1009

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<td class="diff-line-num new_line" data-linenumber="1010" 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">

1010

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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span> <span class="nv" style="color: #008080;">$cluster_verbose_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">-verbose 1 </span><span class="p">";</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1010" 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">

1010

</td>

<td class="diff-line-num new_line" data-linenumber="1011" 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">

1011

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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span> <span class="nv" style="color: #008080;">$cluster_verbose_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">-debug 1 </span><span class="p">";</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1011" 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">

1011

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<td class="diff-line-num new_line old" data-linenumber="1012" 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="LC1011" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span> <span class="p">("</span><span class="s2" style="color: #d14;">OMP_PROC_BIND=</span><span class="si" style="color: #d14;">$ompprocbind</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_clustering </span><span class="si" style="color: #d14;">$cluster_verbose_level</span><span class="s2" style="color: #d14;"> -minspecies </span><span class="si" style="color: #d14;">$minspecies</span><span class="s2" style="color: #d14;"> -ram </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -kmere </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$exactstep3</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -debug </span><span class="si" style="color: #d14;">$debug</span><span class="s2" style="color: #d14;"> -cpus </span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -weighted 1 -conn </span><span class="si" style="color: #d14;">$connectivity</span><span class="s2" style="color: #d14;"> -purity </span><span class="si" style="color: #d14;">$purity</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$clusterOptions</span><span class="s2" style="color: #d14;"> -rmgraph '</span><span class="si" style="color: #d14;">$rm_simgraph</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$simgraph</span><span class="s2" style="color: #d14;">'* >'</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">' </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">?</span> <span class="p">""</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">2>/dev/null</span><span class="p">"));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1012" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1012" 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">

1012

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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="LC1012" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1012" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1013" 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">

1013

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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="LC1013" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span> <span class="p">("</span><span class="s2" style="color: #d14;">OMP_PROC_BIND=</span><span class="si" style="color: #d14;">$ompprocbind</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_clustering </span><span class="si" style="color: #d14;">$cluster_verbose_level</span><span class="s2" style="color: #d14;"> -minspecies </span><span class="si" style="color: #d14;">$minspecies</span><span class="s2" style="color: #d14;"> -ram </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -kmere </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$exactstep3</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -debug </span><span class="si" style="color: #d14;">$debug</span><span class="s2" style="color: #d14;"> -cpus </span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -weighted 1 -conn </span><span class="si" style="color: #d14;">$connectivity</span><span class="s2" style="color: #d14;"> -purity </span><span class="si" style="color: #d14;">$purity</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$clusterOptions</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="si" style="color: #d14;">$clusterOptions</span><span class="p">"</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -rmgraph '</span><span class="si" style="color: #d14;">$rm_simgraph</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$simgraph</span><span class="s2" style="color: #d14;">'* >'</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">' </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">?</span> <span class="p">""</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">2>/dev/null</span><span class="p">"));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1012" 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">

1012

</td>

<td class="diff-line-num new_line" data-linenumber="1014" 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">

1014

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1014" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1013" 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">

1013

</td>

<td class="diff-line-num new_line" data-linenumber="1015" 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">

1015

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1015" class="line" lang="perl">          <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">'proteinortho_clustering' failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Maybe your operating system does not support the statically compiled version, please try recompiling proteinortho with 'make clean' and 'make' (and 'make install PREFIX=...').</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1014" 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">

1014

</td>

<td class="diff-line-num new_line" data-linenumber="1016" 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">

1016

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1016" class="line" lang="perl">        <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1024" 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="1026" 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">@@ -1024,7 +1026,7 @@ sub cluster {</td>

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<td class="diff-line-num old_line" data-linenumber="1024" 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">

1024

</td>

<td class="diff-line-num new_line" data-linenumber="1026" 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">

1026

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1026" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1025" 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">

1025

</td>

<td class="diff-line-num new_line" data-linenumber="1027" 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">

1027

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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> Orthologous groups are written to </span><span class="si" style="color: #d14;">$simtable</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1026" 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">

1026

</td>

<td class="diff-line-num new_line" data-linenumber="1028" 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">

1028

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1028" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">10</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1027" 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">

1027

</td>

<td class="diff-line-num new_line old" data-linenumber="1029" 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="LC1027" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">You can extract the fasta files of each orthology group with</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">proteinortho_grab_proteins.pl -tofiles </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;"> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">' '</span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> (Careful: This will generate a file foreach line in the file </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">).</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1028" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1029" 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">

1029

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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">You can extract the fasta files of each orthology group with</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">proteinortho_grab_proteins.pl </span><span class="p"><span class="idiff left">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$isoform</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">ne</span></span><span class="idiff"> </span><span class="p"><span class="idiff">""</span></span><span class="idiff"> </span><span class="p"><span class="idiff">?</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">--isoform</span></span><span class="p"><span class="idiff">"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"")</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span>-tofiles </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;"> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">' '</span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> (Careful: This will generate a file foreach line in the file </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">).</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1028" 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">

1028

</td>

<td class="diff-line-num new_line" data-linenumber="1030" 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">

1030

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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1029" 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">

1029

</td>

<td class="diff-line-num new_line" data-linenumber="1031" 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">

1031

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<pre style="margin: 0;"> <span id="LC1031" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1030" 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">

1030

</td>

<td class="diff-line-num new_line" data-linenumber="1032" 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">

1032

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<pre style="margin: 0;"> <span id="LC1032" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">(head -n 1 '</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">' && tail -n +2 '</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">' | LC_ALL=C sort -k1,1nr -k2,2nr -k3,3nr ) > '</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">.sort'; mv '</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">.sort' '</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1072" 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="1074" 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">@@ -1072,7 +1074,8 @@ sub cluster {</td>

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<td class="diff-line-num old_line" data-linenumber="1072" 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">

1072

</td>

<td class="diff-line-num new_line" data-linenumber="1074" 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">

1074

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<pre style="margin: 0;"> <span id="LC1074" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cluster_verbose_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1073" 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">

1073

</td>

<td class="diff-line-num new_line" data-linenumber="1075" 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">

1075

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1075" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span> <span class="nv" style="color: #008080;">$cluster_verbose_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">-verbose 1 </span><span class="p">";</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1074" 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">

1074

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<td class="diff-line-num new_line" data-linenumber="1076" 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">

1076

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<pre style="margin: 0;"> <span id="LC1076" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span> <span class="nv" style="color: #008080;">$cluster_verbose_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">-debug 1 </span><span class="p">";</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1075" 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">

1075

</td>

<td class="diff-line-num new_line old" data-linenumber="1077" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1075" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span> <span class="p">("</span><span class="s2" style="color: #d14;">OMP_PROC_BIND=</span><span class="si" style="color: #d14;">$ompprocbind</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_clustering </span><span class="si" style="color: #d14;">$cluster_verbose_level</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$clusterOptions</span><span class="s2" style="color: #d14;"> -minspecies </span><span class="si" style="color: #d14;">$minspecies</span><span class="s2" style="color: #d14;"> -ram </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -kmere </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$exactstep3</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -debug </span><span class="si" style="color: #d14;">$debug</span><span class="s2" style="color: #d14;"> -cpus </span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -weighted 1 -conn </span><span class="si" style="color: #d14;">$connectivity</span><span class="s2" style="color: #d14;"> -purity </span><span class="si" style="color: #d14;">$purity</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$clusterOptions</span><span class="s2" style="color: #d14;"> -rmgraph '</span><span class="si" style="color: #d14;">$rm_syngraph</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$syngraph</span><span class="s2" style="color: #d14;">'* >'</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">' </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">?</span> <span class="p">""</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">2>/dev/null</span><span class="p">"));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1076" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1077" 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">

1077

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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="LC1077" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1076" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1078" 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">

1078

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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="LC1078" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span> <span class="p">("</span><span class="s2" style="color: #d14;">OMP_PROC_BIND=</span><span class="si" style="color: #d14;">$ompprocbind</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_clustering </span><span class="si" style="color: #d14;">$cluster_verbose_level</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$clusterOptions</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="si" style="color: #d14;">$clusterOptions</span><span class="p">"</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -minspecies </span><span class="si" style="color: #d14;">$minspecies</span><span class="s2" style="color: #d14;"> -ram </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -kmere </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$exactstep3</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -debug </span><span class="si" style="color: #d14;">$debug</span><span class="s2" style="color: #d14;"> -cpus </span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -weighted 1 -conn </span><span class="si" style="color: #d14;">$connectivity</span><span class="s2" style="color: #d14;"> -purity </span><span class="si" style="color: #d14;">$purity</span><span class="s2" style="color: #d14;"> -rmgraph '</span><span class="si" style="color: #d14;">$rm_syngraph</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$syngraph</span><span class="s2" style="color: #d14;">'* >'</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">' </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">?</span> <span class="p">""</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">2>/dev/null</span><span class="p">"));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1076" 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">

1076

</td>

<td class="diff-line-num new_line" data-linenumber="1079" 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">

1079

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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1077" 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">

1077

</td>

<td class="diff-line-num new_line" data-linenumber="1080" 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">

1080

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<pre style="margin: 0;"> <span id="LC1080" class="line" lang="perl">        <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">proteinortho_clustering failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Did you use a static version? Maybe your operating system does not support the static compiled version, please recompile 'make clean' and 'make' or 'make USEPRECOMPILEDLAPACK=FALSE'.</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1078" 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">

1078

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<td class="diff-line-num new_line" data-linenumber="1081" 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">

1081

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<pre style="margin: 0;"> <span id="LC1081" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1084" 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="1087" 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">@@ -1084,7 +1087,7 @@ sub cluster {</td>

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<td class="diff-line-num old_line" data-linenumber="1084" 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">

1084

</td>

<td class="diff-line-num new_line" data-linenumber="1087" 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">

1087

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<pre style="margin: 0;"> <span id="LC1087" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1085" 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">

1085

</td>

<td class="diff-line-num new_line" data-linenumber="1088" 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">

1088

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<pre style="margin: 0;"> <span id="LC1088" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">(head -n 1 '</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">' && tail -n +2 '</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">' | LC_ALL=C sort -k1,1nr -k2,2nr -k3,3nr ) > '</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">.sort'; mv '</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">.sort' '</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1086" 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">

1086

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<td class="diff-line-num new_line" data-linenumber="1089" 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">

1089

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1089" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1087" 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">

1087

</td>

<td class="diff-line-num new_line old" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1087" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> Orthologous groups are written to </span><span class="si" style="color: #d14;">$syntable</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">You can extract the fasta files of each orthology group with</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">proteinortho_grab_proteins.pl -tofiles </span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;"> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">' '</span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">(Careful: This will generate a file foreach line in the file </span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">).</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1088" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1090" 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">

1090

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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="LC1090" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> Orthologous groups are written to </span><span class="si" style="color: #d14;">$syntable</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">You can extract the fasta files of each orthology group with</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">proteinortho_grab_proteins.pl </span><span class="p"><span class="idiff left">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$isoform</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">ne</span></span><span class="idiff"> </span><span class="p"><span class="idiff">""</span></span><span class="idiff"> </span><span class="p"><span class="idiff">?</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">--isoform</span></span><span class="p"><span class="idiff">"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"")</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span>-tofiles </span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;"> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">' '</span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">(Careful: This will generate a file foreach line in the file </span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">).</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1088" 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">

1088

</td>

<td class="diff-line-num new_line" data-linenumber="1091" 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">

1091

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1091" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1089" 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">

1089

</td>

<td class="diff-line-num new_line" data-linenumber="1092" 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">

1092

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1092" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$singles</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1090" 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">

1090

</td>

<td class="diff-line-num new_line" data-linenumber="1093" 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">

1093

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1093" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Adding singles...</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1156" 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="1159" 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">@@ -1156,6 +1159,7 @@ Options:</td>

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1156

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<td class="diff-line-num new_line" data-linenumber="1159" 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">

1159

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<pre style="margin: 0;"> <span id="LC1159" class="line" lang="perl"><span class="s2" style="color: #d14;">                      {autoblast|blastp|blastn|tblastx|blastp_legacy|blastn_legacy|tblastx_legacy|diamond|usearch|ublast|lastp|lastn|rapsearch|topaz|blatp|blatn|mmseqsp|mmseqsn}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1157" 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">

1157

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<td class="diff-line-num new_line" data-linenumber="1160" 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">

1160

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<pre style="margin: 0;"> <span id="LC1160" class="line" lang="perl"><span class="s2" style="color: #d14;">                      The suffix 'p' or 'n' indicates aminoacid fasta files (p) or nucleotide fasta files (n).</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1158" 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">

1158

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<td class="diff-line-num new_line" data-linenumber="1161" 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">

1161

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<pre style="margin: 0;"> <span id="LC1161" class="line" lang="perl"><span class="s2" style="color: #d14;">                      The suffix '_legacy' indicates legacy blastall (otherwise blast+ is used).</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1159" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1162" 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">

1162

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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="perl"><span class="s2" style="color: #d14;">         -checkfasta  Checks if the given fasta files are compatible with the algorithm of -p</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1159" 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">

1159

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<td class="diff-line-num new_line" data-linenumber="1163" 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">

1163

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<pre style="margin: 0;"> <span id="LC1163" class="line" lang="perl"><span class="s2" style="color: #d14;">         -e=          E-value for blast [default: 1e-05]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1160" 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">

1160

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<td class="diff-line-num new_line" data-linenumber="1164" 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">

1164

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<pre style="margin: 0;"> <span id="LC1164" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1161" 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">

1161

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<td class="diff-line-num new_line" data-linenumber="1165" 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">

1165

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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="perl"><span class="s2" style="color: #d14;">         [Synteny options]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1226" 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="1230" 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">@@ -1226,7 +1230,7 @@ Options:</td>

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<td class="diff-line-num old_line" data-linenumber="1226" 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">

1226

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<td class="diff-line-num new_line" data-linenumber="1230" 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="LC1230" class="line" lang="perl"><span class="s2" style="color: #d14;">                        topaz : Only for protein files!</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1227" 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">

1227

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<td class="diff-line-num new_line" data-linenumber="1231" 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="LC1231" class="line" lang="perl"><span class="s2" style="color: #d14;">                        blat* : Blat family. blatp : For protein files! blatn : For dna files! blatx : For dna files!</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1228" 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">

1228

</td>

<td class="diff-line-num new_line" data-linenumber="1232" 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">

1232

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<pre style="margin: 0;"> <span id="LC1232" class="line" lang="perl"><span class="s2" style="color: #d14;">                        mmseqs* : mmseqs family. mmseqsp : For protein files! mmseqsn : For dna files! blatx : For dna files!</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1229" 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">

1229

</td>

<td class="diff-line-num new_line old" data-linenumber="1233" 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="LC1229" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1230" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1233" 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">

1233

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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="perl"><span class="s2" style="color: #d14;">         -checkfasta  Checks if the given fasta files are compatible with the algorithm of -p</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1230" 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">

1230

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<td class="diff-line-num new_line" data-linenumber="1234" 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">

1234

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<pre style="margin: 0;"> <span id="LC1234" class="line" lang="perl"><span class="s2" style="color: #d14;">         -e=          E-value for blast [default: 1e-05]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1231" 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">

1231

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<td class="diff-line-num new_line" data-linenumber="1235" 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">

1235

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<pre style="margin: 0;"> <span id="LC1235" class="line" lang="perl"><span class="s2" style="color: #d14;">         -selfblast   apply selfblast, detects paralogs without orthologs</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1232" 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">

1232

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<td class="diff-line-num new_line" data-linenumber="1236" 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">

1236

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<pre style="margin: 0;"> <span id="LC1236" class="line" lang="perl"><span class="s2" style="color: #d14;">         -sim=        min. similarity for additional hits (0..1) [default: 0.95]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1878" 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="1882" 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">@@ -1878,7 +1882,7 @@ sub get_legal_matches {</td>

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<td class="diff-line-num new_line" data-linenumber="1882" 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">

1882

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<pre style="margin: 0;"> <span id="LC1882" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1883" 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="LC1883" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1880" 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">

1880

</td>

<td class="diff-line-num new_line" data-linenumber="1884" 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">

1884

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1884" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$query_id</span><span class="p">}</span> <span class="p">){</span> <span class="nv" style="color: #008080;">$query_id</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$query_id</span><span class="p">};</span> <span class="p">}</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1881" 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">

1881

</td>

<td class="diff-line-num new_line old" data-linenumber="1885" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1881" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$subject_id</span><span class="p">}</span> <span class="p">){</span> <span class="nv" style="color: #008080;">$<span class="idiff left right">query</span>_id</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$subject_id</span><span class="p">};</span> <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1882" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1885" 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">

1885

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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="LC1885" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$subject_id</span><span class="p">}</span> <span class="p">){</span> <span class="nv" style="color: #008080;">$<span class="idiff left right">subject</span>_id</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$subject_id</span><span class="p">};</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1882" 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">

1882

</td>

<td class="diff-line-num new_line" data-linenumber="1886" 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">

1886

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<pre style="margin: 0;"> <span id="LC1886" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1883" 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">

1883

</td>

<td class="diff-line-num new_line" data-linenumber="1887" 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">

1887

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1887" class="line" lang="perl">   </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1884" 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">

1884

</td>

<td class="diff-line-num new_line" data-linenumber="1888" 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">

1888

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<pre style="margin: 0;"> <span id="LC1888" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># It hit itself (only during selfblast)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2602" 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="2606" 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">@@ -2602,7 +2606,7 @@ sub check_bins {</td>

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<td class="diff-line-num old_line" data-linenumber="2602" 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">

2602

</td>

<td class="diff-line-num new_line" data-linenumber="2606" 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">

2606

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2606" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Check plausibility of files</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2603" 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">

2603

</td>

<td class="diff-line-num new_line" data-linenumber="2607" 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">

2607

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2607" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">check_files</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2604" 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">

2604

</td>

<td class="diff-line-num new_line" data-linenumber="2608" 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">

2608

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2608" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$selfblast</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span>   <span class="p">{</span><span class="nv" style="color: #008080;">&print_usage</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">I need at least two files to compare something!</span><span class="p">");}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2605" 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">

2605

</td>

<td class="diff-line-num new_line old" data-linenumber="2609" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2605" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Checking input files</span><span class="p">";</span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$checkfasta</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> <span class="idiff left right">very carefully (-check</span>).</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2606" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2609" 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">

2609

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2609" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Checking input files</span><span class="p">";</span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$checkfasta</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> <span class="idiff left right">carefully (-checkfasta</span>).</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2606" 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">

2606

</td>

<td class="diff-line-num new_line" data-linenumber="2610" 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">

2610

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2610" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2607" 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">

2607

</td>

<td class="diff-line-num new_line" data-linenumber="2611" 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">

2611

</td>

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<pre style="margin: 0;"> <span id="LC2611" class="line" lang="perl">  <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2608" 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">

2608

</td>

<td class="diff-line-num new_line" data-linenumber="2612" 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">

2612

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<pre style="margin: 0;"> <span id="LC2612" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Checking </span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">... </span><span class="p">";}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2664" 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="2668" 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">@@ -2664,12 +2668,13 @@ sub read_details {</td>

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<pre style="margin: 0;"> <span id="LC2668" class="line" lang="perl">        <span class="nv" style="color: #008080;">$isoform_mapping_ncbiuniprot_correction</span><span class="p">{</span><span class="nv" style="color: #008080;">&convertUniprotAndNCBI</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">)}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="2665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2669" 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="LC2669" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2670" 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="LC2670" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">trinity</span><span class="p">"){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="2671" 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="LC2667" class="line" lang="perl"><span class="idiff left">        </span><span class="nv" style="color: #008080;"><span class="idiff">$curLine</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=~</span></span><span class="sr" style="color: #009926;"><span class="idiff">s/_i[0-9]+$//g</span></span><span class="p"><span class="idiff right">;</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="2671" 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="LC2668" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^([^ ]+)_i[0-9]+(<span class="idiff left right"> </span>|$)/</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2671" 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="LC2671" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2672" 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="LC2672" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^([^ ]+)_i[0-9]+(<span class="idiff left right">[^0-9].*</span>|$)/</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2673" 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="LC2673" class="line" lang="perl">          <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$iso</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2674" 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="LC2674" class="line" lang="perl">          <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">#chomp only removes last \n newline, now also \r are removed and all occurences</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2675" 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="LC2675" class="line" lang="perl">          <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2676" 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="LC2676" class="line" lang="perl">          <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\s.*//</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2677" 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="LC2677" class="line" lang="perl">          <span class="nv" style="color: #008080;">$iso</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2678" 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="LC2678" class="line" lang="perl">          <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$iso</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2679" 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="LC2679" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC2680" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">found isoform '</span><span class="si" style="color: #d14;">$curLine</span><span class="s2" style="color: #d14;">' => '</span><span class="si" style="color: #d14;">$iso</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2780,9 +2785,9 @@ sub read_details {</td>

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2780

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<td class="diff-line-num new_line" data-linenumber="2785" 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">

2785

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<pre style="margin: 0;"> <span id="LC2785" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$allowedAlphabet</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">n</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span> <span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2781" 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">

2781

</td>

<td class="diff-line-num new_line" data-linenumber="2786" 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">

2786

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2786" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2782" 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">

2782

</td>

<td class="diff-line-num new_line" data-linenumber="2787" 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">

2787

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<pre style="margin: 0;"> <span id="LC2787" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">1</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2783" 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">

2783

</td>

<td class="diff-line-num new_line old" data-linenumber="2788" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2783" class="line" lang="perl">       <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> [WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> The occurences of <span class="idiff left">ATCGN is less than 50% of in input fasta file '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff right">' in gene</span> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$lastgenename</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'. </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> expects nucleotide characters...</span><span class="si" style="color: #d14;">$NC</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2784" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2788" 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">

2788

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<pre style="margin: 0;">+<span id="LC2788" class="line" lang="perl">       <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> [WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> The occurences of <span class="idiff left">nucleotide characters (ATCGN) is less than 50% of in input fasta file '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff right">' in entry</span> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$lastgenename</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'. </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> expects nucleotide characters...</span><span class="si" style="color: #d14;">$NC</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2784" 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">

2784

</td>

<td class="diff-line-num new_line" data-linenumber="2789" 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">

2789

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<pre style="margin: 0;"> <span id="LC2789" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2785" 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">

2785

</td>

<td class="diff-line-num new_line old" data-linenumber="2790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2785" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> [WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> Found forbidden non-nucleotide character in input fasta file '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$file</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' in <span class="idiff left right">gene</span> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$lastgenename</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'. </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> expects nucleotide characters...</span><span class="si" style="color: #d14;">$NC</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2786" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2790" 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">

2790

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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="LC2790" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> [WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> Found forbidden non-nucleotide character in input fasta file '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$file</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' in <span class="idiff left right">entry</span> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$lastgenename</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'. </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> expects nucleotide characters...</span><span class="si" style="color: #d14;">$NC</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2786" 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">

2786

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<td class="diff-line-num new_line" data-linenumber="2791" 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">

2791

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<pre style="margin: 0;"> <span id="LC2791" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2787" 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">

2787

</td>

<td class="diff-line-num new_line" data-linenumber="2792" 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">

2792

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<pre style="margin: 0;"> <span id="LC2792" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode_pendant</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">})</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$restart_counter</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># only for step = 0 and step 1 you can do a rerun else the DB are missing</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2788" 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">

2788

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<td class="diff-line-num new_line" data-linenumber="2793" 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">

2793

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<pre style="margin: 0;"> <span id="LC2793" class="line" lang="perl">        <span class="nv" style="color: #008080;">$blastmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$blastmode_pendant</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">};</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2798" 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="2803" 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">@@ -2798,9 +2803,9 @@ sub read_details {</td>

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<td class="diff-line-num old_line" data-linenumber="2798" 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">

2798

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<td class="diff-line-num new_line" data-linenumber="2803" 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">

2803

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<pre style="margin: 0;"> <span id="LC2803" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$allowedAlphabet</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">a</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span> <span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2799" 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">

2799

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<td class="diff-line-num new_line" data-linenumber="2804" 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">

2804

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<pre style="margin: 0;"> <span id="LC2804" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2800" 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">

2800

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<td class="diff-line-num new_line" data-linenumber="2805" 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">

2805

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<pre style="margin: 0;"> <span id="LC2805" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">1</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2801" 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">

2801

</td>

<td class="diff-line-num new_line old" data-linenumber="2806" 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="LC2801" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> [WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> The occurences of <span class="idiff left">ATCGN is greater than 80% of '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff right">' in gene</span> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$lastgenename</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'. </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> expects aminoacid characters...</span><span class="si" style="color: #d14;">$NC</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2802" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2806" 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">

2806

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<pre style="margin: 0;">+<span id="LC2806" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> [WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> The occurences of <span class="idiff left">nucleotide characters (ATCGN) is greater than 80% of '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff right">' in entry</span> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$lastgenename</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'. </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> expects aminoacid characters...</span><span class="si" style="color: #d14;">$NC</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2802" 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">

2802

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<td class="diff-line-num new_line" data-linenumber="2807" 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">

2807

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<pre style="margin: 0;"> <span id="LC2807" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2803" 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">

2803

</td>

<td class="diff-line-num new_line old" data-linenumber="2808" 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="LC2803" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">ORANGE [WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> Found forbidden non-aminoacid character in input fasta file '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' in <span class="idiff left right">gene</span> '</span><span class="si" style="color: #d14;">$lastgenename</span><span class="s2" style="color: #d14;">'. </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> expects aminoacid characters</span><span class="si" style="color: #d14;">$NC</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2804" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2808" 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">

2808

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<pre style="margin: 0;">+<span id="LC2808" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">ORANGE [WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> Found forbidden non-aminoacid character in input fasta file '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' in <span class="idiff left right">entry</span> '</span><span class="si" style="color: #d14;">$lastgenename</span><span class="s2" style="color: #d14;">'. </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> expects aminoacid characters</span><span class="si" style="color: #d14;">$NC</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2804" 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">

2804

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<td class="diff-line-num new_line" data-linenumber="2809" 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">

2809

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<pre style="margin: 0;"> <span id="LC2809" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2805" 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">

2805

</td>

<td class="diff-line-num new_line" data-linenumber="2810" 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">

2810

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<pre style="margin: 0;"> <span id="LC2810" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2806" 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">

2806

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<td class="diff-line-num new_line" data-linenumber="2811" 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">

2811

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<pre style="margin: 0;"> <span id="LC2811" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode_pendant</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">})</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$restart_counter</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># only for step = 0 and step 1 you can do a rerun else the DB are missing</span></span>

</pre>

</td>

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<br>

</li>

<li id="ba368ee46e511166051985e745eaa37aea49d150">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/9e6c42c356a281fb5b32f95587dd63adfe0178e4...1486e86627af5db48ee03731c56323b6e19a05ee#ba368ee46e511166051985e745eaa37aea49d150"><strong>src/proteinortho_clustering.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1889" 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="1889" 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">@@ -1889,7 +1889,7 @@ void splitGroups(vector<floattype>& y, vector<unsigned int>& nodes , bool useLap</td>

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1889

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<td class="diff-line-num new_line" data-linenumber="1889" 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">

1889

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<pre style="margin: 0;"> <span id="LC1889" class="line" lang="cpp">                         <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[WARNING]   Failed to partition subgraph with "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">nodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" nodes into ("</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">groupA</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">groupB</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">groupZero</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">") sized groups using lapack, now reiterating with power iteration."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1890" 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">

1890

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<td class="diff-line-num new_line" data-linenumber="1890" 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">

1890

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<pre style="margin: 0;"> <span id="LC1890" class="line" lang="cpp">                         <span class="n" style="color: #333;">getConnectivity</span><span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1891" 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">

1891

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<td class="diff-line-num new_line" data-linenumber="1891" 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">

1891

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<pre style="margin: 0;"> <span id="LC1891" class="line" lang="cpp">                 <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC1892" class="line" lang="cpp">                         <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[<span class="idiff left right">CRITICAL </span>WARNING]   Failed to partition subgraph with "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">nodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" nodes into ("</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">groupA</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">groupB</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">groupZero</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">") sized groups, now using kmere heuristic as fall-back."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC1892" class="line" lang="cpp">                         <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[WARNING]   Failed to partition subgraph with "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">nodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" nodes into ("</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">groupA</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">groupB</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">groupZero</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">") sized groups, now using kmere heuristic as fall-back."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC1893" class="line" lang="cpp">                         <span class="n" style="color: #333;">fallback_justdokmerenow</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC1894" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">do_kmereAlgorithm</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC1895" class="line" lang="cpp">                 <span class="p">}</span></span>

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<br>

</li>

<li id="3439148ea7017354388f7c55043cc84986c1c394">

<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/9e6c42c356a281fb5b32f95587dd63adfe0178e4...1486e86627af5db48ee03731c56323b6e19a05ee#3439148ea7017354388f7c55043cc84986c1c394"><strong>src/proteinortho_grab_proteins.pl</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @author Paul Klemm</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @email klemmp@staff.uni-marburg.de</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @company Bioinformatics, University of Leipzig</span></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @version <span class="idiff left right">4</span></span></span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @date <span class="idiff left right">3-12-2020</span></span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @version <span class="idiff left right">5</span></span></span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @date <span class="idiff left right">1-29-2021</span></span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="perl"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="53" 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="53" 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">@@ -53,6 +53,7 @@ proteinortho_grab_proteins.pl (options) QUERY FASTA1 (FASTA2 ...)</td>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="perl"><span class="s" style="color: #d14;">           -exact        search patters are extended with a \b, that indicates end of word.</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="perl"><span class="s" style="color: #d14;">           -source, -s   adds the filename (FASTA1,...) to the found gene-name</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="perl"><span class="s" style="color: #d14;">           -F=s          char delimiter for multiple identifier if QUERY is a string input (default: ',')</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="perl"><span class="s" style="color: #d14;">           -isoform      if you use proteinortho with --isoform option, then you need to set this option here too. </span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="perl"><span class="s" style="color: #d14;">DESCRIPTION</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="perl"><span class="s" style="color: #d14;"> </span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="101" 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">@@ -100,6 +101,7 @@ ENDUSAGE</td>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$query</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$help</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$tofiles</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$isoform</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$justid</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$prefix</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">></span><span class="p">";</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$doregex</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="117" 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="119" 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">@@ -117,6 +119,7 @@ for(my $v = 0 ; $v < scalar @ARGV_copy ; $v++){</td>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?(source|s)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$source</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?F=(.*)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$del</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?E$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$doregex</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="122" 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="LC122" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?isoform$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$isoform</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="123" 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="LC123" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?exact$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$exact</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="124" 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="LC124" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^-.+/</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$usage</span><span class="p">;</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">ERROR: invalid option </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">!</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="125" 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="LC125" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$query</span><span class="p">)){</span><span class="nv" style="color: #008080;">$query</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">];}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="203" 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="206" 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">@@ -203,7 +206,8 @@ unless(open(my $FH,'<',$query)) {</td>

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<td class="diff-line-num old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="206" 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="LC206" class="line" lang="perl">         <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="204" 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="LC207" class="line" lang="perl"> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="205" 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="LC208" class="line" lang="perl"><span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="209" 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="LC206" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] WARNING The -exact option is mandatory if a proteinortho file is given. -exact is now set.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$exact</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="209" 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="LC209" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] WARNING The -isoform option is not compatible with -exact if a proteinortho file is given. -exact is now unset.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$exact</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="210" 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="LC210" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$isoform</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] WARNING The -exact option is mandatory if a proteinortho file is given. -exact is now set.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$exact</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="211" 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="LC211" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$doregex</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] WARNING The -E option is not allowed if a proteinortho file is given. -E is now unset.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$doregex</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="212" 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="LC212" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="213" 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="LC213" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$query_basename</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$query</span><span class="p">;</span></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -328,7 +332,7 @@ for(my $v = 0 ; $v < scalar @ARGV_copy ; $v++){</td>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$test_match</span> <span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$key</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span></span>

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="perl">                                                         <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] WARNI<span class="idiff left right"> </span>NG The input (</span><span class="si" style="color: #d14;">$key</span><span class="s2" style="color: #d14;">) was found multiple times in the fasta files </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span> <span class="p">?</span> <span class="p">"</span><span class="s2" style="color: #d14;">(maybe try --exact).</span><span class="p">"</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="p">")</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="perl">                                                         <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] WARNING The input (</span><span class="si" style="color: #d14;">$key</span><span class="s2" style="color: #d14;">) was found multiple times in the fasta files </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span> <span class="p">?</span> <span class="p">"</span><span class="s2" style="color: #d14;">(maybe try --exact).</span><span class="p">"</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="p">")</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="perl">                                                 <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>

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