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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/prokka">Debian Med / prokka</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/prokka/commit/6cdfaa4bd08d028ab28b03a998b4c8e62a878aad">6cdfaa4b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-07-23T16:36:42Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.13.7+dfsg</pre>
</li>
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#f60133a4cdbf56999bb8caf361866b541c61b231">
bin/prokka
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f60133a4cdbf56999bb8caf361866b541c61b231">
<a href="https://salsa.debian.org/med-team/prokka/commit/6cdfaa4bd08d028ab28b03a998b4c8e62a878aad#f60133a4cdbf56999bb8caf361866b541c61b231"><strong>bin/prokka</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,7 +45,7 @@ my @CMDLINE = ($0, @ARGV);</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$OPSYS</span> <span class="o" style="font-weight: 600;">=</span> <span class="vg" style="color: #008080;">$^O</span><span class="p">;</span></span>
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46
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$BINDIR</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$FindBin</span><span class="s2" style="color: #d14;">::RealBin/../binaries/</span><span class="si" style="color: #d14;">$OPSYS</span><span class="p">";</span></span>
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<td class="diff-line-num old_line" data-linenumber="47" 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">
47
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<td class="diff-line-num new_line" data-linenumber="47" 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">
47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$EXE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">FindBin::</span><span class="nv" style="color: #008080;">RealScript</span><span class="p">;</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">1.13.<span class="idiff left right">3</span></span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">1.13.<span class="idiff left right">7</span></span><span class="p">";</span></span>
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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">Torsten Seemann <torsten.seemann@gmail.com></span><span class="p">';</span></span>
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50
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$URL</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">https://github.com/tseemann/prokka</span><span class="p">';</span></span>
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<td class="diff-line-num old_line" data-linenumber="51" 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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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$PROKKA_PMID</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">24642063</span><span class="p">';</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -86,8 +86,8 @@ my $BIDEC = '(\d+\.\d+)'; # pattern of NN.NN for versions that can be compared</td>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="87" 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="LC87" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">tools</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">parallel</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">{</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="perl"> <span class="nv" style="color: #008080;">GETVER</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">"</span><span class="s2" style="color: #d14;">parallel --version | grep <span class="idiff left right">'^GNU parallel 2</span>'</span><span class="p">",</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="perl"> <span class="nv" style="color: #008080;">REGEXP</span> <span class="o" style="font-weight: 600;">=></span> <span class="sx" style="color: #d14;">qr/<span class="idiff left right">GNU </span>parallel (\d+)/</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="89" 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="LC89" class="line" lang="perl"> <span class="nv" style="color: #008080;">GETVER</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">"</span><span class="s2" style="color: #d14;">parallel --version | grep <span class="idiff left">-E 'parallel 2[0-9]{7}</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff right">$</span>'</span><span class="p">",</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="perl"> <span class="nv" style="color: #008080;">REGEXP</span> <span class="o" style="font-weight: 600;">=></span> <span class="sx" style="color: #d14;">qr/parallel (\d+)/</span><span class="p">,</span></span>
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91
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="perl"> <span class="nv" style="color: #008080;">MINVER</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">"</span><span class="s2" style="color: #d14;">20130422</span><span class="p">",</span></span>
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92
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="perl"> <span class="nv" style="color: #008080;">NEEDED</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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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="perl"> <span class="p">},</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">@@ -156,13 +156,13 @@ my %tools = (</td>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">blastp</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">{</span></span>
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157
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="perl"> <span class="nv" style="color: #008080;">GETVER</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">"</span><span class="s2" style="color: #d14;">blastp -version</span><span class="p">",</span></span>
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158
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="perl"> <span class="nv" style="color: #008080;">REGEXP</span> <span class="o" style="font-weight: 600;">=></span> <span class="sx" style="color: #d14;">qr/blastp:\s+($BIDEC)/</span><span class="p">,</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="perl"> <span class="nv" style="color: #008080;">MINVER</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">"</span><span class="s2" style="color: #d14;">2.<span class="idiff left right">2</span></span><span class="p">",</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="perl"> <span class="nv" style="color: #008080;">MINVER</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">"</span><span class="s2" style="color: #d14;">2.<span class="idiff left right">8</span></span><span class="p">",</span></span>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="perl"> <span class="nv" style="color: #008080;">NEEDED</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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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="perl"> <span class="p">},</span></span>
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162
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">makeblastdb</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">{</span></span>
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163
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="perl"> <span class="nv" style="color: #008080;">GETVER</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">"</span><span class="s2" style="color: #d14;">makeblastdb -version</span><span class="p">",</span></span>
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164
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="perl"> <span class="nv" style="color: #008080;">REGEXP</span> <span class="o" style="font-weight: 600;">=></span> <span class="sx" style="color: #d14;">qr/makeblastdb:\s+($BIDEC)/</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="perl"> <span class="nv" style="color: #008080;">MINVER</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">"</span><span class="s2" style="color: #d14;">2.<span class="idiff left right">2</span></span><span class="p">",</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="perl"> <span class="nv" style="color: #008080;">MINVER</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">"</span><span class="s2" style="color: #d14;">2.<span class="idiff left right">8</span></span><span class="p">",</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="perl"> <span class="nv" style="color: #008080;">NEEDED</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;"># only if --proteins used</span></span>
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="perl"> <span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">tbl2asn</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">{</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">@@ -1342,7 +1342,7 @@ for my $sid (@seq) {</td>
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="perl"> <span class="nv" style="color: #008080;">$count</span><span class="p">{</span> <span class="nv" style="color: #008080;">$f</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">primary_tag</span> <span class="p">}</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="perl"> <span class="p">}</span></span>
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1344
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1345" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ft</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">count</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ft</span> <span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">sort</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">keys</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">count</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1346" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">printf</span> <span class="p">"</span><span class="s2" style="color: #d14;">%s: %d</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span> <span class="nv" style="color: #008080;">$ft</span><span class="p">,</span> <span class="nv" style="color: #008080;">$count</span><span class="p">{</span><span class="nv" style="color: #008080;">$ft</span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC1347" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1348" class="line" lang="perl"></span>
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