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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/hyphy">Debian Med / hyphy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/commit/a6bb7eb332e252c39e090b4cc20c87e0a1f115da">a6bb7eb3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-06T12:30:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5.1+dfsg</pre>
</li>
</ul>
<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#07aceb8d215a75908cea626d9c80bc2a7c06639c">
src/core/global_things.cpp
</a>
</li>
<li class="file-stats">
<a href="#a2cd4af628c072bf1be79488bcc65091ecca9295">
src/core/strings.cpp
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/hyphy/commit/a6bb7eb332e252c39e090b4cc20c87e0a1f115da#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" 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="189" 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">@@ -189,7 +189,8 @@ endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)</td>
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189
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<td class="diff-line-num new_line" data-linenumber="189" 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">
189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>CMAKE_CXX_COMPILER_ID MATCHES <span class="s2" style="color: #d14;">"Clang"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="190" 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">
190
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<td class="diff-line-num new_line" data-linenumber="190" 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">
190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>DEFAULT_COMPILE_FLAGS <span class="s2" style="color: #d14;">"-fsigned-char -O3"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="191" 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">
191
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<td class="diff-line-num new_line" data-linenumber="191" 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">
191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">PCL_CHECK_FOR_AVX</span><span class="p">()</span></span>
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<td class="diff-line-num old old_line" data-linenumber="192" 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">
192
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<td class="diff-line-num new_line old" data-linenumber="192" 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="LC192" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">HAVE_AVX_EXTENSIONS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cmake"></span>
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<td class="diff-line-num new old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">HAVE_AVX_EXTENSIONS</span><span class="si" style="color: #d14;">}</span> AND NOT <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">NOAVX</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
193
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<td class="diff-line-num new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>DEFAULT_COMPILE_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_COMPILE_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -march=native -mtune=native -mavx"</span><span class="p">)</span></span>
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194
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<td class="diff-line-num new_line" data-linenumber="195" 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">
195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span> <span class="p">(</span>-D_SLKP_USE_AVX_INTRINSICS<span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="195" 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">
195
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<td class="diff-line-num new_line" data-linenumber="196" 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">
196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">PCL_CHECK_FOR_FMA3</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="197" 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="198" 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">@@ -197,7 +198,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")</td>
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197
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>DEFAULT_COMPILE_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DEFAULT_COMPILE_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -mfma"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
198
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<td class="diff-line-num new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span> <span class="p">(</span>-D_SLKP_USE_FMA3_INTRINSICS<span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
199
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<td class="diff-line-num new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">HAVE_FMA3</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">else</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">HAVE_AVX_EXTENSIONS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">else</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">HAVE_AVX_EXTENSIONS</span><span class="si" style="color: #d14;">}</span><span class="idiff left"> AND NOT </span><span class="si" style="color: #d14;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">NOAVX</span></span><span class="si" style="color: #d14;"><span class="idiff right">}</span></span><span class="p">)</span></span>
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201
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<td class="diff-line-num new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">PCL_CHECK_FOR_SSE3</span><span class="p">()</span></span>
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202
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">HAVE_SSE3_EXTENSIONS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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203
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<td class="diff-line-num new_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">
204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span> <span class="p">(</span>-D_SLKP_USE_SSE_INTRINSICS<span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="290" 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="291" 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">@@ -290,7 +291,7 @@ if(NOT NODE)</td>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">message</span><span class="p">(</span><span class="s2" style="color: #d14;">"Node not installed; API documentation will not be generated"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">else</span><span class="p">(</span>NOT NODE<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_custom_target</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="cmake"> docs<span class="idiff left right"> ALL</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cmake"> docs</span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cmake"> rm -rf ./docs && npm install -g documentation@4 && documentation build --polyglot -f md ./res/TemplateBatchFiles/libv3/**/*.bf -o ./docs.md</span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cmake"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span>NOT NODE<span class="p">)</span></span>
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<li id="07aceb8d215a75908cea626d9c80bc2a7c06639c">
<a href="https://salsa.debian.org/med-team/hyphy/commit/a6bb7eb332e252c39e090b4cc20c87e0a1f115da#07aceb8d215a75908cea626d9c80bc2a7c06639c"><strong>src/core/global_things.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_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>
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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">@@ -119,7 +119,7 @@ namespace hy_global {</td>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringDatasetRefIndexError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Dataset index reference out of range"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringMatrixExportError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Export matrix called with a non-polynomial matrix argument"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringNullOperand</span> <span class="p">(</span><span class="s" style="color: #d14;">"Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">kHyPhyVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.<span class="idiff left right">0</span>"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">kHyPhyVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.<span class="idiff left right">1</span>"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">kNoneToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"None"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">kNullToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"null"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/commit/a6bb7eb332e252c39e090b4cc20c87e0a1f115da#a2cd4af628c072bf1be79488bcc65091ecca9295"><strong>src/core/strings.cpp</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">@@ -52,7 +52,7 @@</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">compileDate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__DATE__</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">__HYPHY__VERSION__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.<span class="idiff left right">0</span>"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">__HYPHY__VERSION__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.<span class="idiff left right">1</span>"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">hy_global</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"></span>
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