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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/psortb">Debian Med / psortb</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/psortb/commit/9497b2a1db6dbb5e1d7acb873c6323c82b4858d9">9497b2a1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-26T19:53:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.6+dfsg</pre>
</li>
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#e8b97e771c860d11d27b1a63cf43f3cb9c03a081">
psort/bin/psort
</a>
</li>
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<h4>Changes:</h4>
<li id="e8b97e771c860d11d27b1a63cf43f3cb9c03a081">
<a href="https://salsa.debian.org/med-team/psortb/commit/9497b2a1db6dbb5e1d7acb873c6323c82b4858d9#e8b97e771c860d11d27b1a63cf43f3cb9c03a081"><strong>psort/bin/psort</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/perl</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">IO::</span><span class="nv" style="color: teal;">String</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Getopt::</span><span class="nv" style="color: teal;">Long</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#use Data::Dumper;</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">lib</span> <span class="s" style="color: #d14;">'../lib'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::Tools::PSort::Report::</span><span class="nv" style="color: teal;">Formatter</span><span class="p">;</span></span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::Tools::</span><span class="nv" style="color: teal;">PSort</span><span class="p">;</span></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: teal;">SeqIO</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::Tools::PSort::</span><span class="nv" style="color: teal;">Constants</span> <span class="sx" style="color: #d14;">qw(:all)</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="perl"></span>
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<td class="diff-line-num old old_line" data-linenumber="8" 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="LC8" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Getopt::</span><span class="nv" style="color: teal;">Long</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9" 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="13" 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="LC9" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Data::</span><span class="nv" style="color: teal;">Dumper</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">strict</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$ENV</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,8 +61,8 @@ MAIN: {</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$psort_analysis</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'psort'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$psort_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'bayes'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$root</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'/usr/local/psortb<span class="idiff left right">-3.0</span>'</span><span class="p">;</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$blastdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'/usr/local/<span class="idiff left right">bio/blast</span>'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$root</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'/usr/local/psortb<span class="idiff left right">3</span>'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$blastdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'/usr/local/<span class="idiff left right">pkg/blast-2.2.26//bin</span>'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$pftools</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'/usr/local/bin/'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$pfscan_module</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Profile'</span><span class="p">;</span></span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="361" 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">@@ -361,11 +363,10 @@ MAIN: {</td>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="perl"> <span class="p">[</span><span class="s" style="color: #d14;">'CWSVM_a'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sub </span><span class="p">{</span><span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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362
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="perl"> <span class="p">[</span><span class="s" style="color: #d14;">'Signal_a'</span><span class="p">]</span></span>
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="perl"> <span class="p">]]]]]]]]]);</span> <span class="c1" style="color: #998; font-style: italic;"># add a bracket back later</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="perl"><span class="idiff left right"> </span><span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"We should never be here.\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="perl"> <span class="idiff left right"> </span><span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="perl"><span class="idiff left right"> </span><span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"We should never be here.\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="perl"></span>
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Create a new PSort object.</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"* Using \"$server\" as remote PSort server\n"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="379" 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">@@ -378,18 +379,19 @@ MAIN: {</td>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="perl"></span>
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Figure out whether or not we're getting the sequences from a file or from</span></span>
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># STDIN and open up a Bio::SeqIO on it.</span></span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$seqfh</span><span class="p">;</span></span>
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381
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$fname</span><span class="p">)</span> <span class="p">{</span></span>
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382
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384
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<pre style="margin: 0;"> <span id="LC384" 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: teal;">f</span> <span class="nv" style="color: teal;">$fname</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">r</span> <span class="nv" style="color: teal;">$fname</span><span class="p">))</span> <span class="p">{</span></span>
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383
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"* Reading sequences from file \"$fname\"\n"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$verbose</span><span class="p">);</span></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: teal;">SEQS</span><span class="p">,</span> <span class="nv" style="color: teal;">$fname</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: open $fname: $!\n"</span><span class="p">);</span></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="perl"> <span class="nv" style="color: teal;">$sio</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: teal;">SeqIO</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">fh</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\*</span><span class="nv" style="color: teal;">SEQS</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: teal;">$format</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="perl"> <span class="nv" style="color: teal;">$seqfh</span> <span class="o" style="font-weight: 600;">=</span> <span class="sr" style="color: #009926;">make_seq_input_uppercase($fnam</span><span class="nv" style="color: teal;">e</span><span class="p">);</span></span>
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386
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: file \"$fname\" doesn't exist or isn't readable\n"</span><span class="p">);</span></span>
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388
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="perl"> <span class="p">}</span></span>
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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390
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"* Reading sequences from STDIN\n"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$verbose</span><span class="p">);</span></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="perl"> <span class="nv" style="color: teal;">$s<span class="idiff left">io</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">Bio::</span></span><span class="nv" style="color: teal;"><span class="idiff">SeqIO</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: teal;"><span class="idiff">fh</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">\*</span></span><span class="bp" style="color: #999;"><span class="idiff">STDIN</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$format</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="perl"> <span class="nv" style="color: teal;">$s<span class="idiff left">eqfh</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="sr" style="color: #009926;"><span class="idiff">make_seq_input_uppercas</span></span><span class="nv" style="color: teal;"><span class="idiff">e</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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392
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="perl"> <span class="nv" style="color: teal;">$sio</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: teal;">SeqIO</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">fh</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: teal;">$seqfh</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: teal;">$format</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="perl"></span>
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Ready for prime time - go forth and PSort.</span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$format</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nn" style="color: #555;">Bio::Tools::PSort::Report::</span><span class="nv" style="color: teal;">Formatter</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">@@ -404,3 +406,35 @@ MAIN: {</td>
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="perl"> <span class="p">}</span></span>
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="nv" style="color: teal;">$format</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nv" style="color: teal;">$output</span><span class="p">,</span> <span class="p">{</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">cutoff</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: teal;">$cutoff</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">gram</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: teal;">$gram</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="sr" style="color: #009926;">mcutoff => $divergent, -psort => $psort, -skiplocalizations => \@skippedlocali</span><span class="nv" style="color: teal;">zations</span><span class="p">},</span> <span class="nv" style="color: teal;">@reps</span><span class="p">));</span></span>
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="perl"><span class="p">}</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="perl"></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">make_seq_input_uppercase</span> <span class="p">{</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$seqinput</span><span class="p">;</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$fname</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: teal;">SEQS</span><span class="p">,</span> <span class="nv" style="color: teal;">$fname</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: open $fname: $!\n"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#$seqinput = <SEQS>;</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="perl"> <span class="nv" style="color: teal;">$seqinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span> <span class="nb" style="color: #0086b3;">local</span> <span class="vg" style="color: teal;">$/</span><span class="p">;</span> <span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: teal;">SEQS</span><span class="o" style="font-weight: 600;">></span> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="perl"> <span class="p">}</span> </span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="perl"> <span class="nv" style="color: teal;">$seqinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># hack to convert sequences (not headers) to uppercase (lowercase </span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># seems to bring back no psortb results)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@seqs2uc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="s" style="color: #d14;">">"</span><span class="p">,</span> <span class="nv" style="color: teal;">$seqinput</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="427" 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">
427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">shift</span><span class="p">(</span><span class="nv" style="color: teal;">@seqs2uc</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># remove blank first element (after doing split on > where > is the first character)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="407" 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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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="perl"></span>
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<td class="diff-line-num new old_line" data-linenumber="407" 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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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$uc_seqs</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$header_seq</span> <span class="p">(</span><span class="nv" style="color: teal;">@seqs2uc</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="431" 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">
431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$h1</span><span class="p">,</span> <span class="nv" style="color: teal;">$s1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/[\n\r]+/</span><span class="p">,</span> <span class="nv" style="color: teal;">$header_seq</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$s1</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/[a-z]/</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="433" 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">
433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="perl"> <span class="nv" style="color: teal;">$s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nv" style="color: teal;">$s1</span><span class="p">);</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="perl"> <span class="p">}</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="perl"> <span class="nv" style="color: teal;">$uc_seqs</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">">$h1\n$s1"</span><span class="p">;</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="perl"> <span class="p">}</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="perl"> </span>
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<td class="diff-line-num new new_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$seqfh</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nn" style="color: #555;">IO::</span><span class="nv" style="color: teal;">String</span><span class="p">(</span><span class="nv" style="color: teal;">$uc_seqs</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="nv" style="color: teal;">$seqfh</span><span class="p">);</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="perl"><span class="p">}</span></span></pre>
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