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<h3>
Benjamin Redelings pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/bali-phy">Debian Med / bali-phy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243">aed48311</a></strong>
<div>
<span>by Benjamin Redelings</span>
<i>at 2019-01-22T19:00:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.4.1+dfsg</pre>
</li>
</ul>
<h4>25 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
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<li class="file-stats">
<a href="#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa">
meson.build
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<li class="file-stats">
<a href="#f0c9a876cc18faf1fae8cc6f4d9b130fb6e2a10d">
src/alignment/index-matrix.H
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</li>
<li class="file-stats">
<a href="#23b769dc6cc44940bd94198a014d2ebe9abf3da3">
src/models/TreeInterface.cc
</a>
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<li class="file-stats">
<a href="#dd886b71ff4df5dd2b908de62e98200255cf6459">
src/parser/desugar-case.cc
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</li>
<li class="file-stats">
<a href="#d3080ca51f439f576222fc20bb9459e84cd0f607">
src/startup/help.cc
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<li class="file-stats">
<a href="#6be081bd9e677ad95656d2d37c5c2f1c3ccde672">
src/tools/draw-tree.cc
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<li class="file-stats">
<a href="#37666462b8f49cb96329d3e4e6dbe261d31efddd">
src/tools/stats-table.cc
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<li class="file-stats">
<a href="#bb52f76309192cfe9936ce78dc5bda794d15595c">
src/tools/trees-distances.cc
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<li class="file-stats">
<a href="#1badd0f18c1d91b1f1706720d1d7e006bce65e7b">
src/tools/trees-to-SRQ.cc
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<li class="file-stats">
<a href="#457699a05c6d1eb2414226c72fd33fca3b83bb41">
src/tree/tree.H
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<li class="file-stats">
<a href="#10921a300751b1b806cb673070713fed7a9a48df">
tests/optimizer/10/error
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<li class="file-stats">
<a href="#350842e8b98897de91968a95a596f15715247073">
tests/optimizer/13/error
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<li class="file-stats">
<a href="#71d4ba4aa2ade0be0201b551f36ae10e5cad0a91">
tests/optimizer/14/error
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<li class="file-stats">
<a href="#ffaffeb3315b1b072da0f40f0785af275365b78d">
tests/optimizer/15/error
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<li class="file-stats">
<a href="#ad92d71064b15a0dc68df88ba7a0fec2318e356a">
tests/optimizer/3/error
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<li class="file-stats">
<a href="#2a797a1af6104cd6f7eb593b52873c060c523a26">
tests/optimizer/4/error
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<li class="file-stats">
<a href="#cbb74fd3bbeebdefeef3befe5a356e1d1b76629c">
tests/optimizer/5/error
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<li class="file-stats">
<a href="#0e442ef641a17a126c36c74a7e518bd0c54c552e">
tests/optimizer/6/error
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<li class="file-stats">
<a href="#4127e6d65cc0bb6ff8a8494de29ba6972df9fc56">
tests/optimizer/8/error
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<li class="file-stats">
<a href="#68938df3aacdf8825824d465947d810393c7bb59">
tests/optimizer/9/error
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<li class="file-stats">
<a href="#39948791e085b1ce2d36609d32dbe6607fc49ab5">
tests/optimizer/eta-reduction/error
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<li class="file-stats">
<a href="#883e47681d2493e7953865b90983822c0cc66989">
tests/optimizer/pat-bind/error
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<li class="file-stats">
<a href="#0a7a25af70cfe923e86bd848a309c6358a430b55">
<span class="new-file">
+
tests/optimizer/update-tests.sh
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<li class="file-stats">
<a href="#394227ffae1a3a9bc762baab5da76dfc3d17547e">
tests/run-tests.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" 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="58" 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">@@ -58,7 +58,7 @@ before_install:</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ -n "${C_COMPILER}" ]; then export CC="${C_COMPILER}"; fi</span></span>
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<td class="diff-line-num 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">
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ -n "${CXX_COMPILER}" ]; then export CXX="${CXX_COMPILER}"; fi</span></span>
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<td class="diff-line-num old_line" data-linenumber="60" 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="60" 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="LC60" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update && brew install meson; fi</span></span>
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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget https://github.com/ninja-build/ninja/releases/download/v1.8.2/ninja-linux.zip && unzip -q ninja-linux.zip -d ~/bin && pyenv local 3.<span class="idiff left right">6</span> && pip3 install meson; fi</span></span>
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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget https://github.com/ninja-build/ninja/releases/download/v1.8.2/ninja-linux.zip && unzip -q ninja-linux.zip -d ~/bin && pyenv local 3.<span class="idiff left right">7</span> && pip3 install meson; fi</span></span>
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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="yaml"></span>
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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="yaml"><span class="na" style="color: teal;">script</span><span class="pi">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">meson build --prefix=$HOME/local</span></span>
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<li id="0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa">
<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa"><strong>meson.build</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">project('bali-phy', ['cpp','c'],</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> version: '3.4',</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> version: '3.4<span class="idiff left right">.1</span>',</span>
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<td class="diff-line-num old_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> default_options : [</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> 'buildtype=release',</span>
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<td class="diff-line-num old_line" data-linenumber="5" 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">
5
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<td class="diff-line-num new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext"> 'cpp_std=c++14'</span>
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<li id="f0c9a876cc18faf1fae8cc6f4d9b130fb6e2a10d">
<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#f0c9a876cc18faf1fae8cc6f4d9b130fb6e2a10d"><strong>src/alignment/index-matrix.H</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" 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="35" 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">@@ -35,7 +35,7 @@ struct Edge</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">edge_comp</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span><span class="p">()(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Edge</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">E1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Edge</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">E2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span><span class="p">()(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Edge</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">E1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Edge</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">E2</span><span class="p">)</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">E1</span><span class="p">.</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">E2</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"><span class="p">};</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#23b769dc6cc44940bd94198a014d2ebe9abf3da3"><strong>src/models/TreeInterface.cc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "tree/tree.H"</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "TreeInterface.H"</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "models/parameters.H"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"></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">@@ -482,7 +483,7 @@ std::string write(const TreeInterface& T, int root, const std::vector<double>& L</td>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">branches</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">target</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="cpp"> <span class="n" style="color: #333;">names2</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left">"'"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">names2</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">n</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="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"'</span>:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">L</span><span class="p">[</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">undirected</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)]);</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"> <span class="n" style="color: #333;">names2</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">names2</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">n</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="s" style="color: #d14;"><span class="idiff right">"</span>:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">L</span><span class="p">[</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">undirected</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)]);</span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">names2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="cpp"><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">@@ -491,15 +492,18 @@ std::string write(const TreeInterface& T, int root, const std::vector<double>& L</td>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TreeInterface</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">T</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">print_lengths</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="cpp"><span class="p">{</span></span>
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494
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">root</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;">// T.target(0);</span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">names2</span><span class="p">;</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">names</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp"> <span class="n" style="color: #333;">names2</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">escape_for_newick</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">));</span></span>
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">print_lengths</span><span class="p">)</span></span>
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">L</span><span class="p">;</span></span>
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501
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">n_branches</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="cpp"> <span class="n" style="color: #333;">L</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">branch_length</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">L</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">L</span><span class="p">,</span> <span class="n" style="color: #333;">names<span class="idiff left right">2</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">names<span class="idiff left right">2</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="cpp"><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">edges_connecting_to_node</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Tree</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">T</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#dd886b71ff4df5dd2b908de62e98200255cf6459"><strong>src/parser/desugar-case.cc</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">@@ -289,7 +289,7 @@ failable_expression desugar_state::match_empty(const vector<expression_ref>& x,</td>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">failable_expression</span> <span class="n" style="color: #333;">E</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fail_identity</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reverse</span><span class="p">(</span><span class="n" style="color: #333;">equations</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">E</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">combine</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">E</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">e</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">rhs</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">E</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">combine</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">e</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rhs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">E</span></span><span class="p">);</span></span>
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">E</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#d3080ca51f439f576222fc20bb9459e84cd0f607"><strong>src/startup/help.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="408" 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">@@ -408,7 +408,7 @@ void help_topics(std::ostream& o, const ptree& help)</td>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">subtopics</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_subtopics</span><span class="p">(</span><span class="n" style="color: #333;">help</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">subtopics</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"functions"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"To help on one of the following topics, run `bali-phy help "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">underline</span><span class="p">(</span><span class="s" style="color: #d14;">"topic"</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"`</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"To <span class="idiff left right">see </span>help on one of the following topics, run `bali-phy help "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">underline</span><span class="p">(</span><span class="s" style="color: #d14;">"topic"</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"`</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">show_options</span><span class="p">(</span><span class="n" style="color: #333;">subtopics</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="cpp"> <span class="n" style="color: #333;">o</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="LC414" class="line" lang="cpp"> <span class="n" style="color: #333;">o</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="440" 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="440" 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">@@ -440,15 +440,17 @@ void show_help(const string& topic, const vector<fs::path>& package_paths)</td>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="cpp"> <span class="n" style="color: #333;">Rules</span> <span class="n" style="color: #333;">R</span><span class="p">(</span><span class="n" style="color: #333;">package_paths</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">topic</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"functions"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">func_names</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">R</span><span class="p">.</span><span class="n" style="color: #333;">get_rules</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">get_child_optional</span><span class="p">(</span><span class="s" style="color: #d14;">"name"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">get_child</span><span class="p">(</span><span class="s" style="color: #d14;">"name"</span><span class="p">).</span><span class="n" style="color: #333;">get_value</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">result_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unparse_type</span><span class="p">(</span><span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">get_child</span><span class="p">(</span><span class="s" style="color: #d14;">"result_type"</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">name</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;">result_type</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"> <span class="n" style="color: #333;">func_names</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">show_options</span><span class="p">(</span><span class="n" style="color: #333;">func_names</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#6be081bd9e677ad95656d2d37c5c2f1c3ccde672"><strong>src/tools/draw-tree.cc</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">@@ -23,6 +23,10 @@</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <fstream></span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef M_PI</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define M_PI 3.14159265358979323846</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// FIXME - Add a command-line option to turn on clouds.</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - Actually draw arrows on type 2 edges.</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - Figure out how to use boost's Kamada-Kawai layout.</span></span>
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<li id="37666462b8f49cb96329d3e4e6dbe261d31efddd">
<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#37666462b8f49cb96329d3e4e6dbe261d31efddd"><strong>src/tools/stats-table.cc</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">@@ -28,7 +28,10 @@</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/optional.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optional</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC31" 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;">std</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">dynamic_bitset</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" 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">@@ -68,7 +71,7 @@ void write_header(std::ostream& o, const vector<string>& headers)</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">headers</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> </span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">headers</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="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">o</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="102" 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="105" 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">@@ -102,8 +105,8 @@ optional<pair<unsigned,unsigned>> is_numeric_range(const string& s, unsigned n)</td>
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102
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">none</span><span class="p">;</span></span>
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103
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="p">}</span></span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="mi" style="color: #099;">1U</span><span class="p">,</span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="mi" style="color: #099;">1U</span><span class="p">,</span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span><span class="p">{</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">};</span></span>
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108
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"></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">@@ -172,7 +175,7 @@ bool read_entries(const string& line, const vector<int>& indices, char delim, ve</td>
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172
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"></span>
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173
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><></span> </span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">load_file</span><span class="p">(</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">file</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">skip</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">subsample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">load_file</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">file</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">skip</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">subsample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">ignore</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">select</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp"><span class="p">{</span></span>
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Read in headers from file</span></span>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#bb52f76309192cfe9936ce78dc5bda794d15595c"><strong>src/tools/trees-distances.cc</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">@@ -40,9 +40,16 @@</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">po</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">po</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variables_map</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC43" 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;">std</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" 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;">statistics</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">valarray</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optional</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></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">@@ -739,7 +746,7 @@ int main(int argc,char* argv[])</td>
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// set the window size</span></span>
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_lag</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">(</span><span class="n" style="color: #333;">trees</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="mf" style="color: #099;">10.0</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1.0</span> <span class="p">)</span> <span class="p">);</span></span>
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748
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"max-lag"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC742" class="line" lang="cpp"> <span class="n" style="color: #333;">max_lag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">max_lag</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="s" style="color: #d14;">"max-lag"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="cpp"> <span class="n" style="color: #333;">max_lag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">max_lag</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="s" style="color: #d14;">"max-lag"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bound the max_lag</span></span>
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_lag</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">trees</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="mi" style="color: #099;">2</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">@@ -875,7 +882,7 @@ int main(int argc,char* argv[])</td>
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875
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">trees1</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">required_hits</span><span class="p">;</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> </span>
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">distance</span><span class="p">(</span><span class="n" style="color: #333;">trees1</span><span class="p">[</span><span class="n" style="color: #333;">t</span><span class="p">],</span><span class="n" style="color: #333;">trees2</span><span class="p">,</span><span class="n" style="color: #333;">metric_fn</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC878" class="line" lang="cpp"> <span class="n" style="color: #333;">closest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">closest</span><span class="p">,</span><span class="n" style="color: #333;">d</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="cpp"> <span class="n" style="color: #333;">closest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">closest</span><span class="p">,</span><span class="n" style="color: #333;">d</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="cpp"></span>
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887
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">x1</span><span class="p">)</span> <span class="p">{</span></span>
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888
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">required_hits</span> <span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">4</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">@@ -31,7 +31,6 @@</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "tree/tree-util.H"</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "statistics.H"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC34" 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;">std</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/program_options.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">po</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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">@@ -40,7 +39,10 @@ using po::variables_map;</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">valarray</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optional</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"></span>
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<li id="457699a05c6d1eb2414226c72fd33fca3b83bb41">
<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#457699a05c6d1eb2414226c72fd33fca3b83bb41"><strong>src/tree/tree.H</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">@@ -725,4 +725,6 @@ void remove_sub_branches(Tree& T);</td>
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="c"><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">same_topology_and_node_and_branch_numbers</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Tree</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">T1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Tree</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">T2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">escape_for_newick</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">unescape_from_newick</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC730" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#10921a300751b1b806cb673070713fed7a9a48df"><strong>tests/optimizer/10/error</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">size = 1 Test.#0 = Foreign.Vector.listFromString Test.#11</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">size = 1 Test.#10 = Test.#<span class="idiff left right">4</span>:Test.#3</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">size = 1 Test.#10 = Test.#<span class="idiff left right">8</span>:Test.#3</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">size = 1 Test.#11 = "case: failed pattern match"</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">size = 1 Test.#1145 = Test.#<span class="idiff left right">13</span>:Test.#10</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">size = 1 Test.#1145 = Test.#<span class="idiff left right">7</span>:Test.#10</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">size = 1 Test.#1151 = 10</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">size = 1 Test.#1153 = 2</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">size = 1 Test.#13 = 'y'</span>
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8
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">size = 1 Test.#2 = '!'</span>
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9
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">size = 1 Test.#3 = Test.#2:[]</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">size = 1 Test.#4 = 'o'</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">size = 1 Test.#5 = Prelude:error Test.#1145</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">size = 1 Test.#6 = Prelude:error Test.#0</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">size = 1 Test.f = \#8 -> case #8 of {#1148:#1149 -> #1148,[] -> Test.#5,_ -> Test.#6}</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">size = 3 Test.g = \#1149 -> let {#1150 = 10} in let {#1152 = case #1149 of {#1148:#1153 -> #1148,[] -> Test.#5,_ -> Test.#6}} in Prelude:add #1150 #1152</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">size = 1 Test.#4 = Prelude:error Test.#0</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">size = 1 Test.#7 = 'y'</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">size = 1 Test.#8 = 'o'</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">size = 1 Test.#9 = Prelude:error Test.#1145</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">size = 1 Test.f = \#6 -> case #6 of {#1148:#1149 -> #1148,[] -> Test.#9,_ -> Test.#4}</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">size = 3 Test.g = \#1149 -> let {#1150 = 10} in let {#1152 = case #1149 of {#1148:#1153 -> #1148,[] -> Test.#9,_ -> Test.#4}} in Prelude:add #1150 #1152</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">size = 1 Test.h = Prelude:add Test.#1151 Test.#1153</span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#350842e8b98897de91968a95a596f15715247073"><strong>tests/optimizer/13/error</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">size = 2 Test.f = \#<span class="idiff left right">9 -> let {#1 = case #9 of {#166:#167 -> #166,[] -> Data.List.#22,_ -> Data.List.#23}} in \#10 #11 -> case #1 of {Data.Bool.True -> #10,_ -> #11</span>}</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">size = 2 Test.g = \#1<span class="idiff left right">3 #14 #15 -> case #15 of {#166:#167 -> case #166 of {Data.Bool.True -> #13,_ -> #14},[] -> case Data.List.#22 of {Data.Bool.True -> #13,_ -> #14},_ -> case Data.List.#23 of {Data.Bool.True -> #13,_ -> #14</span>}}</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">size = 2 Test.f = \#<span class="idiff left right">7 -> let {#1 = case #7 of {#166:#167 -> #166,[] -> Data.List.#55,_ -> Data.List.#17}} in \#8 #9 -> case #1 of {Data.Bool.True -> #8,_ -> #9</span>}</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">size = 2 Test.g = \#1<span class="idiff left right">0 #11 #12 -> case #12 of {#166:#167 -> case #166 of {Data.Bool.True -> #10,_ -> #11},[] -> case Data.List.#55 of {Data.Bool.True -> #10,_ -> #11},_ -> case Data.List.#17 of {Data.Bool.True -> #10,_ -> #11</span>}}</span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#71d4ba4aa2ade0be0201b551f36ae10e5cad0a91"><strong>tests/optimizer/14/error</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">size = 1 Main.#0 = Main.#<span class="idiff left right">18</span>:[]</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">size = 1 Main.#0 = Main.#<span class="idiff left right">25</span>:[]</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">size = 1 Main.#1 = 'f'</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">size = 1 Main.#1141 = Foreign.Vector.listFromString Main.#1<span class="idiff left right">7</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">size = 1 Main.#1144 = Foreign.Vector.listFromString Main.#<span class="idiff left right">33</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">size = 1 Main.#1141 = Foreign.Vector.listFromString Main.#1<span class="idiff left right">2</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">size = 1 Main.#1144 = Foreign.Vector.listFromString Main.#<span class="idiff left right">24</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">size = 1 Main.#1148 = Main.#1:[]</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">size = 1 Main.#1151 = "Main.f3: pattern match failure"</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">size = 1 Main.#1152 = Foreign.Vector.listFromString Main.#1151</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">size = 1 Main.#1<span class="idiff left right">3 = Prelude:error Main.#1141</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">size = 1 Main.#<span class="idiff left right">17</span> = "case: failed pattern match"</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">size = 1 Main.#<span class="idiff left right">18</span> = 'f'</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">size = 1 Main.#33 = <span class="idiff left right">"case: failed pattern match"</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">size = 1 Main.#4<span class="idiff left right">5 = Prelude:error Main.#1148</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">size = 1 Main.#<span class="idiff left right">59</span> = Prelude:error Main.#1152</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">size = 1 Main.#<span class="idiff left right">6 = Prelude:error Main.#1144</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">size = 7 Main.f = \#2<span class="idiff left right">9 #30 -> let {fail1 = case #29 of {[] -> Main.fail2#0,#10:#11 -> case #30 of {[] -> #10:[],#3:#4 -> Main.fail2#0,_ -> Main.#6},_ -> Main.#13}} in case #29 of {#24:#25 -> case #30 of {#1151:#1152 -> Data.List.++ #25</span> #1152,_ -> fail1},_ -> fail1}</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">size = 4 Main.f2 = \#1150 #1151 -> case #1150 of {#<span class="idiff left right">35:#36 -> case #1151 of {#37:#38 -> Data.List.++ #36 #38,[] -> #35:[],_ -> Main.#45},_ -> Main.#45</span>}</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">size = 4 Main.f3 = \#<span class="idiff left right">47 #48 -> case #47 of {#49:#50 -> case #48 of {#51:#52 -> Data.List.++ #50 #52,[] -> #49:[],_ -> Main.#59},_ -> Main.#59</span>}</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">size = 1 Main.#1<span class="idiff left right">2 = "case: failed pattern match"</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">size = 1 Main.#<span class="idiff left right">24</span> = "case: failed pattern match"</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">size = 1 Main.#<span class="idiff left right">25</span> = 'f'</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">size = 1 Main.#33 = <span class="idiff left right">Prelude:error Main.#1148</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">size = 1 Main.#4<span class="idiff left right"> = Prelude:error Main.#1144</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">size = 1 Main.#<span class="idiff left right">45</span> = Prelude:error Main.#1152</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">size = 1 Main.#<span class="idiff left right">9 = Prelude:error Main.#1141</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">size = 7 Main.f = \#2<span class="idiff left right">1 #22 -> let {fail1 = case #21 of {[] -> Main.fail2#0,#7:#8 -> case #22 of {[] -> #7:[],#1151:#3 -> Main.fail2#0,_ -> Main.#4},_ -> Main.#9}} in case #21 of {#17:#18 -> case #22 of {#1151:#1152 -> Data.List.++ #18</span> #1152,_ -> fail1},_ -> fail1}</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">size = 4 Main.f2 = \#1150 #1151 -> case #1150 of {#<span class="idiff left right">1152:#26 -> case #1151 of {#27:#28 -> Data.List.++ #26 #28,[] -> #1152:[],_ -> Main.#33},_ -> Main.#33</span>}</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">size = 4 Main.f3 = \#<span class="idiff left right">35 #36 -> case #35 of {#37:#38 -> case #36 of {#39:#40 -> Data.List.++ #38 #40,[] -> #37:[],_ -> Main.#45},_ -> Main.#45</span>}</span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">size = 1 Main.fail2#0 = Prelude:error Main.#0</span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#ffaffeb3315b1b072da0f40f0785af275365b78d"><strong>tests/optimizer/15/error</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">size = 1 Test.#0 = Foreign.Vector.listFromString Test.#<span class="idiff left right">9</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">size = 1 Test.#<span class="idiff left right">5</span> = Prelude:error Test.#0</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">size = 1 Test.#<span class="idiff left right">9</span> = "case: failed pattern match"</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">size = 2 Test.f = \#<span class="idiff left right">7 -> case #7 of {(#1142, #3) -> 2,_ -> Test.#5</span>}</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">size = 1 Test.#0 = Foreign.Vector.listFromString Test.#<span class="idiff left right">7</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">size = 1 Test.#<span class="idiff left right">4</span> = Prelude:error Test.#0</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">size = 1 Test.#<span class="idiff left right">7</span> = "case: failed pattern match"</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">size = 2 Test.f = \#<span class="idiff left right">6 -> case #6 of {(#1142, #3) -> 2,_ -> Test.#4</span>}</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">size = 1 Test.#0 = 10</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">size = 1 Test.#1142 = 3</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">size = 1 Test.#<span class="idiff left right">4</span> = Prelude:add Test.#0 Test.#1142</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">size = 0 Test.f = \#<span class="idiff left right">3 -> Test.#4</span></span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">size = 1 Test.#<span class="idiff left right">3</span> = Prelude:add Test.#0 Test.#1142</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">size = 0 Test.f = \#<span class="idiff left right">2 -> Test.#3</span></span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">size = 1 Test.#0 = Foreign.Vector.listFromString Test.#12</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">size = 1 Test.#12 = "case: failed pattern match"</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">size = 1 Test.#<span class="idiff left right">8</span> = Prelude:error Test.#0</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">size = 2 Test.f = \#<span class="idiff left right">10 -> case #10 of {0 -> 1,2 -> 3,_ -> Test.#8</span>}</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">size = 1 Test.#<span class="idiff left right">5</span> = Prelude:error Test.#0</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">size = 2 Test.f = \#<span class="idiff left right">7 -> case #7 of {0 -> 1,2 -> 3,_ -> Test.#5</span>}</span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">size = 1 Test.#0 = Foreign.Vector.listFromString Test.#1<span class="idiff left right">8</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">size = 1 Test.#1<span class="idiff left right">2 = Prelude:error Test.#0</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">size = 1 Test.#<span class="idiff left right">18 = "case: failed pattern match"</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">size = 2 Test.f = \#1<span class="idiff left right">4 -> case #14 of {#8:#9 -> #9,[] -> [],_ -> Test.#12</span>}</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">size = 1 Test.#0 = Foreign.Vector.listFromString Test.#1<span class="idiff left right">3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">size = 1 Test.#1<span class="idiff left right">3 = "case: failed pattern match"</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">size = 1 Test.#<span class="idiff left right">9 = Prelude:error Test.#0</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">size = 2 Test.f = \#1<span class="idiff left right">1 -> case #11 of {#7:#8 -> #8,[] -> [],_ -> Test.#9</span>}</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">size = 1 Test.#0 = 10</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">size = 1 Test.#2 = Prelude:negate Test.#0</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">size = 0 Test.f = \#1 -> Test.#2</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">size = 1 Test.g = \#<span class="idiff left right">3 #4 -> let {#1144 = \#1 -> #4} in Compiler.Base.IOAndPass #3</span> #1144</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">size = 1 Test.h = \#<span class="idiff left right">6 #7 -> #6:#7</span></span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">size = 1 Test.g = \#<span class="idiff left right">1140 #3 -> let {#1144 = \#26 -> #3} in Compiler.Base.IOAndPass #1140</span> #1144</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">size = 1 Test.h = \#<span class="idiff left right">4 #5 -> #4:#5</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">@@ -2,5 +2,5 @@ size = 1 Test.#0 = Prelude:add Test.#1139 Test.#1</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">size = 1 Test.#1 = 20</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">size = 1 Test.#1139 = 10</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">size = 1 Test.#1140 = 10</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">size = 1 Test.#<span class="idiff left right">2</span> = Prelude:add Test.#0 Test.#1140</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">size = 0 Test.f = \#1141 -> Test.#<span class="idiff left right">2</span></span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">size = 1 Test.#<span class="idiff left right">3</span> = Prelude:add Test.#0 Test.#1140</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">size = 0 Test.f = \#1141 -> Test.#<span class="idiff left right">3</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">size = 3 Test.f = \#<span class="idiff left right">8 -> let {#1142 = let {#1 = 2} in Prelude:add #8</span> #1} in Prelude:multiply #1142 #1142</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">size = 3 Test.f = \#<span class="idiff left right">6 -> let {#1142 = let {#1 = 2} in Prelude:add #6</span> #1} in Prelude:multiply #1142 #1142</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">size = 0 Test.f = Test.g</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">size = 2 Test.g = \#<span class="idiff left right">3 -> let {#1 = Test.g #3</span>} in Test.f #1</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">size = 2 Test.g = \#<span class="idiff left right">2 -> let {#1 = Test.g #2</span>} in Test.f #1</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">size = 1 Test.#0 = 1</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">size = 1 Test.#1 = 2</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">size = 4 Test.#127 = \#1147 -> case #1147 of {(#1148, #1149) -> let {#1151 = Prelude:multiply #1148 #1148} in let {#1152 = []} in #1151:#1152,_ -> []}</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">size = 1 Test.#2 = (Test.#0, Test.#1)</span>
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4
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">size = 1 Test.#3 = 3</span>
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5
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">size = 1 Test.#4 = 4</span>
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6
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">size = 1 Test.#5 = (Test.#3, Test.#4)</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">size = 4 Test.#511 = \#1147 -> case #1147 of {(#1148, #1149) -> let {#1151 = Prelude:multiply #1148 #1148} in let {#1152 = []} in #1151:#1152,_ -> []}</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">size = 1 Test.#515 = Test.#2:Test.#6</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">size = 2 Test.#516 = Data.List.map Test.#511 Test.#515</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">size = 1 Test.#509 = Test.#2:Test.#6</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">size = 2 Test.#510 = Data.List.map Test.#127 Test.#509</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">size = 1 Test.#6 = Test.#5:[]</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">size = 1 Test.x = 1</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">size = 1 Test.xxs = Data.List.concat Test.#51<span class="idiff left right">6</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">size = 1 Test.xxs = Data.List.concat Test.#51<span class="idiff left right">0</span></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">size = 1 Test.xys = Test.#2:Test.#6</span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">size = 1 Test.y = 2</span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#0a7a25af70cfe923e86bd848a309c6358a430b55"><strong>tests/optimizer/update-tests.sh</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span><span class="nb" style="color: #0086b3;">dir </span><span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">*</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$dir</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"> <span class="o" style="font-weight: 600;">(</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$dir</span><span class="s2" style="color: #d14;">"</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: navy;">-e</span> xfail <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cp </span>obtained-error error</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="o" style="font-weight: 600;">)</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/commit/aed48311225a724428b1afa91653390fd2b12243#394227ffae1a3a9bc762baab5da76dfc3d17547e"><strong>tests/run-tests.py</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/python3</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/<span class="idiff left right">env </span>python3</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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