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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/plast">Debian Med / plast</a>
</h3>
<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/plast/commit/044166896682adeae5f87fd888ea023032fee6eb">04416689</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-07-13T18:13:54+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.3.2+dfsg</pre>
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<h4>10 changed files:</h4>
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<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<a href="#69e27356ef629022720d868ab0c0e3394775b6c1">
<span class="deleted-file">
−
README
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
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+
README.md
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<li class="file-stats">
<a href="#f0d736ec9106d9024b36b9b3dab8d72b0b5476fb">
scripts/plast.sh
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<li class="file-stats">
<a href="#7668f77519cef1846c97e7373ee4fc843a9ff474">
scripts/test-plast.sh
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<li class="file-stats">
<a href="#fe8f483085a3e4dc1011be130c0dc584e00ad949">
src/alignment/visitors/impl/XmlOutputVisitor.cpp
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<li class="file-stats">
<a href="#22510018ad9a1cdd22f27113db3d9601c86c1382">
src/misc/api/PlastStrings.hpp
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<li class="file-stats">
<a href="#d0c450869b24540c5f4e051198967dd133e3d042">
src/misc/api/PlastStringsRepository.hpp
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<li class="file-stats">
<a href="#2e1c407e5dc580aace165b8cea11b4ac9736dd3d">
src/misc/api/version.hpp
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<li class="file-stats">
<a href="#6dffb965ac5862061255c6ea5b3b5cef6ce34546">
src/tools/PlastCmd.cpp
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<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/plast/commit/044166896682adeae5f87fd888ea023032fee6eb#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" 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="12" 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">@@ -12,7 +12,7 @@ find_package (JNI REQUIRED)</td>
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12
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<td class="diff-line-num new_line" data-linenumber="12" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">################################################################################</span></span>
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<td class="diff-line-num old_line" data-linenumber="13" 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="13" 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="LC13" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>plast_VERSION_MAJOR 2<span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="14" 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="14" 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="LC14" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>plast_VERSION_MINOR 3<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>plast_VERSION_PATCH <span class="idiff left right">1</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="16" 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="15" 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="LC15" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>plast_VERSION_PATCH <span class="idiff left right">2</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="16" 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="16" 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="LC16" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>plast-version <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">plast_VERSION_MAJOR</span><span class="si" style="color: #d14;">}</span>.<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">plast_VERSION_MINOR</span><span class="si" style="color: #d14;">}</span>.<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">plast_VERSION_PATCH</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="17" 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="LC17" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>plast-date <span class="s2" style="color: #d14;">"xxxx-xx-xx"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="18" 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="LC18" class="line" lang="cmake"></span>
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<li id="69e27356ef629022720d868ab0c0e3394775b6c1">
<a href="https://salsa.debian.org/med-team/plast/commit/044166896682adeae5f87fd888ea023032fee6eb#69e27356ef629022720d868ab0c0e3394775b6c1"><strong>README</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">PLAST - c++ project</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">===================</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">This project contains:</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">----------------------</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">1. C++/11 source code ('src' directory);</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">2. sample Fasta files to test software ('db' directory);</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">3. cmake file to compile the project. </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Requirements</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">------------</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">1. cmake 2.6 or above;</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">2. gcc 4.4+ (Linux), gcc/Mingw64 (Windows) or clang (MacOSX) compiler.</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Compiling PLAST</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">---------------</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">The PLAST library can be compiled in a terminal with the cmake tool. </span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">As a result of source code compilation, one should get a dynamic library (in 'build/lib' </span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">directory) and a commend-line tool (in 'build/bin' directory). You can test resulting</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">binary using the 'test-plast.sh' script provided in 'scripts' directory.</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">Requirements: </span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> * Linux: </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> kernel 2.6+ </span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> gcc 4.4+ </span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> cmake 2.8+</span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> * MacOS: </span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> OS 10.7+ </span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> cmake 2.8+ </span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> XCode 4+ and its command-line development tools </span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> * Windows: </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> Seven+</span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> cmake 2.8+</span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> MinGW-64 environment (since gcc is required to compile PLAST)</span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">Be aware that the more recent OS version you use, the more faster PLAST will be.</span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">Once the source archive has been retrieved and unzipped, one just has to do:</span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">Linux:</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> mkdir build</span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> cd build</span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> cmake ..</span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> make</span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">MacOS: </span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> set CC=gcc</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> set CXX=g++</span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> mkdir build</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> cd build</span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> cmake ..</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> make</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">Windows: (use MinGW-MSYS to run a real Unix shell)</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> mkdir build</span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> cd build</span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> cmake -G "MSYS Makefiles" ..</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> make</span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">Developer documentation</span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext">-----------------------</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">See https://project.inria.fr/plast/developer-guide/</span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">License</span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">-------</span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext"></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">PLAST is free software; you can redistribute it and/or modify it under the Affero GPL v3 </span>
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<td class="diff-line-num old old_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">license. See http://www.gnu.org/licenses/agpl-3.0.en.html</span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/plast/commit/044166896682adeae5f87fd888ea023032fee6eb#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">PLAST Library</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=============</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gh" style="color: #999;">What is PLAST?</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">PLAST stands for Parallel Local Sequence Alignment Search Tool and is was published in <span class="p">[</span><span class="nv" style="color: teal;">BMC Bioinformatics, 2009</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.biomedcentral.com/1471-2105/10/329</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown">PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown">Relying on unique software architecture, PLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">PLAST is a general purpose sequence comparison tool providing the following benefits:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">*</span> PLAST is a high-performance sequence comparison tool designed to compare two sets of sequences (query vs. reference),</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">*</span> Reduces the processing time of sequences comparisons while providing highest quality results; i.e. PLAST <span class="ge" style="font-style: italic;">*is*</span> faster than BLAST <span class="ge" style="font-style: italic;">*and*</span> provides its quality,</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">*</span> Contains a fully integrated data filtering engine capable of selecting relevant hits with user-defined criteria (E-Value, identity, coverage, alignment length, etc.),</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p">*</span> Does not require any additional hardware, since it is a software solution. It is easy to install, cost-effective, takes full advantage of multi-core processors and uses a small RAM footprint,</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">*</span> Ready to be used on desktop computer, cluster, cloud as well as within distributed system running Hadoop.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="gh" style="color: #999;">What is PLAST Library?</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="gh" style="color: #999;">----------------------</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">PLAST Library is written in c++/11 and provides all the needed software components required for comparing two sequence databases with the PLAST algorithm.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown">As a library, it should not contain any 'main' function. However, to simplify the use of the library as a command-line tool the library provides:</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="p">1.</span> an API to setup new softwares relying on PLAST;</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="p">2.</span> a main class (tools::PlastCmd.cpp) to directly provide a ready-to-use PLAST command-line tool. </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="gh" style="color: #999;">This project contains:</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"><span class="gh" style="color: #999;">----------------------</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="p">1.</span> C++/11 source code ('src' directory);</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="p">2.</span> CMake file to compile the project on various 64bit OS, such as Linux, MacOSX and Windows;</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="p">3.</span> API documentation ('doc' directory);</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="p">4.</span> sample code snippets illustrating the use of the API ('examples' directory); </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"><span class="p">5.</span> sample Fasta files to test the software ('test/db' directory);</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"><span class="gh" style="color: #999;">Requirements</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"><span class="gh" style="color: #999;">------------</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown">The PLAST library can be compiled in a terminal with the <span class="p">[</span><span class="nv" style="color: teal;">CMake tool</span><span class="p">](</span><span class="sx" style="color: #d14;">https://cmake.org/</span><span class="p">)</span>. </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown">Requirements: </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"><span class="p"> *</span> <span class="gs" style="font-weight: 600;">**Hardware**</span>: Intel/AMD 64bit processor provising SSE2+ instructions set</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="p"> *</span> <span class="gs" style="font-weight: 600;">**Linux**</span>: </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"> kernel 2.6+ ;</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"> gcc 4.4+ ;</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"> cmake 2.8+</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="p"> *</span> <span class="gs" style="font-weight: 600;">**MacOS**</span>: </span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"> OS 10.9+ ;</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"> cmake 2.8+ ; </span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"> XCode and its command-line development tools (clang)</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"><span class="p"> *</span> <span class="gs" style="font-weight: 600;">**Windows**</span>: </span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"> Seven+ ;</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"> cmake 2.8+ ;</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"> MinGW-64 environment (since gcc is required to compile PLAST)</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown">Be aware that the more recent OS version you use, the more faster PLAST will be. Same for gcc/clang.</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"><span class="gh" style="color: #999;">Compiling PLAST binary</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"><span class="gh" style="color: #999;">----------------------</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown">Once the source has been retrieved, one just has to do:</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Linux:*</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cd plast-library</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"><span class="sb" style="color: #d14;"> git checkout stable #see comment [1] below</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"><span class="sb" style="color: #d14;"> mkdir build ; cd build ; cmake .. ; make -j8</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*MacOS:*</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"> cd plast-library</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown"> git checkout stable #see comment <span class="p">[</span><span class="nv" style="color: teal;">1</span><span class="p">]</span> below</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"> set CC=gcc</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"> set CXX=g++</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"> mkdir build ; cd build ; cmake .. ; make -j8</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Windows*</span> (use MinGW-MSYS to run a real Unix shell):</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cd plast-library</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown"><span class="sb" style="color: #d14;"> git checkout stable #see comment [1] below</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"><span class="sb" style="color: #d14;"> mkdir build ; cd build ; cmake -G "MSYS Makefiles" .. ; make -j8</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown">As a result of source code compilation, one should get a dynamic library (in 'build/lib' directory) and a command-line tool (in 'build/bin' directory). </span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown">PlastCmd is a self-contained command-line tool: you can move it anywhere you want, even renaming it; for instance, the PLAST team from Inria provide pre-compiled PLAST binary renamed as 'plast'.</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Comment [1]**</span> - We <span class="ge" style="font-style: italic;">*ALWAYS*</span> advise you to compile PLAST from its stable release:</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"><span class="p">*</span> Github users: after the "git clone", you should run "git checkout stable" before compiling the code. Indeed, compiling PLAST from the master branch is done at your own risk, since this is the development branch of PLAST. As a result, the software may be unstable. This is the reason why PLAST is always tagged with "stable", a tag corresponding to the latest available stable release.</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"><span class="p">*</span> "tar.gz" users: if you retrieve PLAST from its <span class="p">[</span><span class="nv" style="color: teal;">stable archive</span><span class="p">](</span><span class="sx" style="color: #d14;">https://plast.inria.fr/developer-guide/</span><span class="p">)</span> from PLAST web site, you do not have to run 'git checkout stable', since we provide you with a stable archive.</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"><span class="gh" style="color: #999;">Running PLAST cmdline tool</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"> cd plast-library/build/bin</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"> ./PlastCmd -p plastp <span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown"> -i ../../test/db/query.fa <span class="se" style="color: #d14;">\ </span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"> -d ../../test/db/tursiops.fa <span class="se" style="color: #d14;">\ </span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"> -o result.txt</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"><span class="p"> </span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"><span class="p">*</span> -p: the comparison method</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown"><span class="p">*</span> -i: the query</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown"><span class="p">*</span> -d: the reference databank (can be a Fasta file or a Blast databank)</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown"><span class="p">*</span> -o: the result file</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown">More options: see documentation...</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"><span class="gh" style="color: #999;">User documentation</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown">To get PlastCmd inline help:</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown"><span class="sb" style="color: #d14;"> ./PlastCmd -h</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown">PLAST user documentation is <span class="p">[</span><span class="nv" style="color: teal;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://plast.inria.fr/user-guide/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown"><span class="gh" style="color: #999;">Compiling PLAST c++ snippets</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------------------</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown">Developers can see how to use the PLAST c++ API through snippets provided with this project.</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown">Snippets compilation is done as follows:</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="markdown"></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cd plast-library/build</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="markdown"><span class="sb" style="color: #d14;"> make examples</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown">Snippet binaries will be located in 'build/bin'. </span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown">Snippets documentation: <span class="p">[</span><span class="nv" style="color: teal;">http://plast.gforge.inria.fr/docs/cpp/snippets_page.html</span><span class="p">](</span><span class="sx" style="color: #d14;">http://plast.gforge.inria.fr/docs/cpp/snippets_page.html</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="146" 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="LC146" class="line" lang="markdown"><span class="gh" style="color: #999;">Compiling PLAST API documentation</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="149" 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="LC149" class="line" lang="markdown">This documentation is available at <span class="p">[</span><span class="nv" style="color: teal;">http://plast.gforge.inria.fr/docs/cpp/</span><span class="p">](</span><span class="sx" style="color: #d14;">http://plast.gforge.inria.fr/docs/cpp/</span><span class="p">)</span>.</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="markdown">However, you can prepare a local documentation as follows (we suppose you already have compiled PLAST binary, see above):</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cd plast-library/build</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" 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="LC154" class="line" lang="markdown"><span class="sb" style="color: #d14;"> make doc-api</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="markdown"></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="markdown"><span class="gh" style="color: #999;">Developer documentation</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="markdown"><span class="gh" style="color: #999;">-----------------------</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="markdown"></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="markdown">See <span class="p">[</span><span class="nv" style="color: teal;">http://plast.gforge.inria.fr/docs/cpp/</span><span class="p">](</span><span class="sx" style="color: #d14;">http://plast.gforge.inria.fr/docs/cpp/</span><span class="p">)</span>.</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="markdown"></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="markdown"><span class="gh" style="color: #999;">More information and contact</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="markdown"><span class="gh" style="color: #999;">-----------------------------</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown">Please, visit <span class="p">[</span><span class="nv" style="color: teal;">PLAST web site</span><span class="p">](</span><span class="sx" style="color: #d14;">https://plast.inria.fr/</span><span class="p">)</span> for more information and contact (questions regarding the use of PLAST, bug report, feature request, etc.).</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="markdown"></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="markdown"><span class="gh" style="color: #999;">License</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="markdown"><span class="gh" style="color: #999;">-------</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="markdown">PLAST is free software; you can redistribute it and/or modify it under the Affero GPL v3 </span>
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<td class="diff-line-num new new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="markdown">license. See http://www.gnu.org/licenses/agpl-3.0.en.html</span>
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<td class="diff-line-num new new_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="markdown"></span></pre>
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<a href="https://salsa.debian.org/med-team/plast/commit/044166896682adeae5f87fd888ea023032fee6eb#f0d736ec9106d9024b36b9b3dab8d72b0b5476fb"><strong>scripts/plast.sh</strong></a>
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1
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<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1" 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">
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/<span class="idiff left right">ba</span>sh</span></span>
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2
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<td class="diff-line-num new_line" data-linenumber="2" 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">
2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></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">
3
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<td class="diff-line-num new_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">
3
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/*****************************************************************************</span></span>
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4
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<td class="diff-line-num new_line" data-linenumber="4" 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">
4
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * *</span></span>
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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">
5
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * PLAST : Parallel Local Alignment Search Tool *</span></span>
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6
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<td class="diff-line-num new_line old" data-linenumber="6" 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="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * Copyright (c) 2009-2015 Inria *</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * Version 2.3, released November 2015 *</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * Copyright (c) 2009-2015 Inria-Cnrs-Ens *</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * *</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * PLAST is free software; you can redistribute it and/or modify it under *</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * the Affero GPL v3 License *</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * the Affero GPL ver 3 License, that is compatible with the GNU General *</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * Public License *</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * *</span></span>
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<td class="diff-line-num new_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * This program is distributed in the hope that it will be useful, *</span></span>
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12
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<td class="diff-line-num new_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * but WITHOUT ANY WARRANTY; without even the implied warranty of *</span></span>
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13
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * <span class="idiff left right">CECILL version 2</span> License for more details. *</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * <span class="idiff left right">Affero GPL ver 3</span> License for more details. *</span></span>
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15
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<td class="diff-line-num new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># *****************************************************************************/</span></span>
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16
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"></span>
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17
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<td class="diff-line-num new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># start plast execution: you can adapt _scripts_dir as needed if you install</span></span>
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<li id="7668f77519cef1846c97e7373ee4fc843a9ff474">
<a href="https://salsa.debian.org/med-team/plast/commit/044166896682adeae5f87fd888ea023032fee6eb#7668f77519cef1846c97e7373ee4fc843a9ff474"><strong>scripts/test-plast.sh</strong></a>
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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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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/<span class="idiff left right">ba</span>sh</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="shell"></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="shell"><span class="c" style="color: #998; font-style: italic;">#/*****************************************************************************</span></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="shell"><span class="c" style="color: #998; font-style: italic;"># * *</span></span>
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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">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * PLAST : Parallel Local Alignment Search Tool *</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * Copyright (c) 2009-2015 Inria *</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * Version 2.3, released November 2015 *</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * Copyright (c) 2009-2015 Inria-Cnrs-Ens *</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * *</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * PLAST is free software; you can redistribute it and/or modify it under *</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * the Affero GPL v3 License *</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * the Affero GPL ver 3 License, that is compatible with the GNU General *</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * Public License *</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * *</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * This program is distributed in the hope that it will be useful, *</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * but WITHOUT ANY WARRANTY; without even the implied warranty of *</span></span>
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * <span class="idiff left right">CECILL version 2</span> License for more details. *</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># * <span class="idiff left right">Affero GPL ver 3</span> License for more details. *</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># *****************************************************************************/</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># We get the directory of the script (absolute path)</span></span>
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18
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="nv" style="color: teal;">_scripts_dir</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span> <span class="nb" style="color: #0086b3;">cd</span> <span class="nt" style="color: navy;">-P</span> <span class="nt" style="color: navy;">--</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="nt" style="color: navy;">--</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">command</span> <span class="nt" style="color: navy;">-v</span> <span class="nt" style="color: navy;">--</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$0</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">pwd</span> <span class="nt" style="color: navy;">-P</span> <span class="k" style="font-weight: 600;">)</span></span>
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19
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="nv" style="color: teal;">_result</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$_scripts_dir</span>/out.txt</span>
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20
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Start PLAST..."</span></span>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" 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="31" 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">@@ -28,10 +31,17 @@ echo $_cmdline</td>
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28
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"></span>
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29
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: teal;">$_cmdline</span></span>
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30
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" 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> <span class="nv" style="color: teal;">$_result</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"/!</span><span class="se" style="color: #d14;">\ </span><span class="s2" style="color: #d14;">Error: PLAST fails on your system: result file does not exist: </span><span class="nv" style="color: teal;">$_result</span><span class="s2" style="color: #d14;">"</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"></span>
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39
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<pre style="margin: 0;">+<span id="LC39" 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;">-s</span> <span class="nv" style="color: teal;">$_result</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"/!</span><span class="se" style="color: #d14;">\ </span><span class="s2" style="color: #d14;">Error: PLAST fails on your system: result file is empty: </span><span class="nv" style="color: teal;">$_result</span><span class="s2" style="color: #d14;">"</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"></span>
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31
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" done!"</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Read:"</span> <span class="nv" style="color: teal;">$_result</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"*** SUCCESS: result file is: </span><span class="nv" style="color: teal;">$_result</span><span class="s2" style="color: #d14;">"</span></span>
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36
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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37
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"></span></pre>
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<li id="fe8f483085a3e4dc1011be130c0dc584e00ad949">
<a href="https://salsa.debian.org/med-team/plast/commit/044166896682adeae5f87fd888ea023032fee6eb#fe8f483085a3e4dc1011be130c0dc584e00ad949"><strong>src/alignment/visitors/impl/XmlOutputVisitor.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" 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">@@ -25,6 +25,15 @@</td>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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26
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define DEBUG(a) //printf a</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* 2512 = 2*1024+256.</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Why? See FastaSequenceIterator.hpp::commentMaxSize, FileLineIterator.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * where header size is limited to 2048 chars. Then add 256 char for formatting purpose. As a</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * reminder, Plast does not store sequences: the limit of the buffer is ok, since the largest</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * string comes from Hit_definition, aka Fasta header or Blast sequence header.</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</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;">#define MAX_HEADER_SIZE 2048</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define BUFFER_SIZE 2512</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC37" 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="LC38" 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;">database</span><span class="p">;</span></span>
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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="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">alignment</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">@@ -119,16 +128,24 @@ void XmlOutputVisitor::visitQuerySequence (</td>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">PLAST_BUILD_DATE</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">printline</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"<BlastOutput_reference>%s</BlastOutput_reference>"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">STR_PLAST_REFERENCE</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">printline</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"<BlastOutput_db>%s</BlastOutput_db>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">_properties</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getProperty</span> <span class="p">(</span><span class="n" style="color: #333;">STR_OPTION_SUBJECT_URI</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getValue</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* DB like NCBI nr are made of so many volumes that we have a too long string.</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC133" 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;">dbName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_properties</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getProperty</span> <span class="p">(</span><span class="n" style="color: #333;">STR_OPTION_SUBJECT_URI</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getValue</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dbName</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="n" style="color: #333;">MAX_HEADER_SIZE</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">dbName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dbName</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">MAX_HEADER_SIZE</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">dbName</span><span class="p">[</span><span class="n" style="color: #333;">MAX_HEADER_SIZE</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'.'</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="124" 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="137" 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">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">dbName</span><span class="p">[</span><span class="n" style="color: #333;">MAX_HEADER_SIZE</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'.'</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="124" 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="138" 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">
138
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">dbName</span><span class="p">[</span><span class="n" style="color: #333;">MAX_HEADER_SIZE</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'.'</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="124" 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="139" 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">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="124" 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="140" 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">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">printline</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"<BlastOutput_db>%s</BlastOutput_db>"</span><span class="p">,</span> <span class="n" style="color: #333;">dbName</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
124
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<td class="diff-line-num new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">printline</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"<BlastOutput_query-ID>Query_1</BlastOutput_query-ID>"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
125
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<td class="diff-line-num new_line" data-linenumber="142" 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">
142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> <span class="n" style="color: #333;">printline</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"<BlastOutput_query-def>%s</BlastOutput_query-def>"</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDefinition</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="126" 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">
126
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<td class="diff-line-num new_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">printline</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"<BlastOutput_query-len>%d</BlastOutput_query-len>"</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getLength</span><span class="p">());</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="127" 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">
127
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<td class="diff-line-num new_line" data-linenumber="144" 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">
144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="n" style="color: #333;">printline</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"<BlastOutput_query-seq>not specified</BlastOutput_query-seq>"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="128" 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">
128
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<td class="diff-line-num new_line" data-linenumber="145" 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">
145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"> <span class="n" style="color: #333;">printline</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"<BlastOutput_param>"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="129" 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">
129
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<td class="diff-line-num new_line" data-linenumber="146" 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">
146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">printline</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"<Parameters>"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="130" 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">
130
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<td class="diff-line-num new_line old" data-linenumber="147" 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="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">printParameter</span><span class="p">(</span><span class="n" style="color: #333;">STR_OPTION_EVALUE</span><span class="p">,</span> <span class="s" style="color: #d14;">"expect"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="131" 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">
131
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<td class="diff-line-num new_line" data-linenumber="147" 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">
147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">printParameter</span><span class="p">(</span><span class="n" style="color: #333;">STR_OPTION_SCORE_MATRIX</span><span class="p">,</span> <span class="s" style="color: #d14;">"matrix"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="132" 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="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">printParameter</span><span class="p">(</span><span class="n" style="color: #333;">STR_OPTION_EVALUE</span><span class="p">,</span> <span class="s" style="color: #d14;">"expect"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="132" 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">
132
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<td class="diff-line-num new_line" data-linenumber="149" 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">
149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">printParameter</span><span class="p">(</span><span class="n" style="color: #333;">STR_OPTION_OPEN_GAP_COST</span><span class="p">,</span> <span class="s" style="color: #d14;">"gap-open"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="133" 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">
133
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<td class="diff-line-num new_line" data-linenumber="150" 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">
150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">printParameter</span><span class="p">(</span><span class="n" style="color: #333;">STR_OPTION_EXTEND_GAP_COST</span><span class="p">,</span> <span class="s" style="color: #d14;">"gap-extend"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="134" 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">
134
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<td class="diff-line-num new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">printParameter</span><span class="p">(</span><span class="n" style="color: #333;">STR_OPTION_FILTER_QUERY</span><span class="p">,</span> <span class="s" style="color: #d14;">"filter"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="243" 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="260" 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">@@ -243,13 +260,12 @@ void XmlOutputVisitor::printline (size_t depth, const char* format, ...)</td>
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<td class="diff-line-num old_line" data-linenumber="243" 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">
243
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<td class="diff-line-num new_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** We dump the indentation. */</span></span>
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<pre style="margin: 0;"> <span id="LC261" 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;">size_t</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;">depth</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 class="p">{</span> <span class="n" style="color: #333;">getStream</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">1024</span></span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">BUFFER_SIZE</span></span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"></span>
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">va_list</span> <span class="n" style="color: #333;">va</span><span class="p">;</span></span>
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249
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">va_start</span> <span class="p">(</span><span class="n" style="color: #333;">va</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">);</span></span>
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250
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="n" style="color: #333;">vsprintf</span> <span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="n" style="color: #333;">va</span><span class="p">);</span></span>
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">va_end</span> <span class="p">(</span><span class="n" style="color: #333;">va</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp"> <span class="n" style="color: #333;">getStream</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">buffer</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="LC270" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/plast/commit/044166896682adeae5f87fd888ea023032fee6eb#22510018ad9a1cdd22f27113db3d9601c86c1382"><strong>src/misc/api/PlastStrings.hpp</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">@@ -90,7 +90,7 @@ namespace misc {</td>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_OPTION_SMALLGAP_THRESHOLD misc::StringRepository::m_STR_OPTION_SMALLGAP_THRESHOLD ()</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** "-b" Command Line option giving the bandwith size used during the small gap algorithm.</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** "-b" Command Line option giving the bandwi<span class="idiff left right">d</span>th size used during the small gap algorithm.</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Integer value.</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_OPTION_SMALLGAP_BAND_WITH misc::StringRepository::m_STR_OPTION_SMALLGAP_BAND_WITH ()</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">@@ -406,7 +406,7 @@ namespace misc {</td>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_HELP_UNGAP_NEIGHBOUR_LENGTH misc::StringRepository::m_STR_HELP_UNGAP_NEIGHBOUR_LENGTH () // Size of neighbourhood peforming ungapped extension</span></span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_HELP_UNGAP_SCORE_THRESHOLD misc::StringRepository::m_STR_HELP_UNGAP_SCORE_THRESHOLD () // Ungapped threshold trigger a small gapped extension</span></span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_HELP_SMALLGAP_THRESHOLD misc::StringRepository::m_STR_HELP_SMALLGAP_THRESHOLD () // threshold for small gapped extension</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_HELP_SMALLGAP_BAND_WITH misc::StringRepository::m_STR_HELP_SMALLGAP_BAND_WITH () // bandwith for small gapped extension</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_HELP_SMALLGAP_BAND_WITH misc::StringRepository::m_STR_HELP_SMALLGAP_BAND_WITH () // bandwi<span class="idiff left right">d</span>th for small gapped extension</span></span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_HELP_NB_PROCESSORS misc::StringRepository::m_STR_HELP_NB_PROCESSORS () // Number of processors to use</span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_HELP_OPEN_GAP_COST misc::StringRepository::m_STR_HELP_OPEN_GAP_COST () // Cost to open a gap</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_HELP_EXTEND_GAP_COST misc::StringRepository::m_STR_HELP_EXTEND_GAP_COST () // Cost to extend a gap</span></span>
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<a href="https://salsa.debian.org/med-team/plast/commit/044166896682adeae5f87fd888ea023032fee6eb#d0c450869b24540c5f4e051198967dd133e3d042"><strong>src/misc/api/PlastStringsRepository.hpp</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">@@ -127,7 +127,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_UNGAP_NEIGHBOUR_LENGTH</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ObsfucatedString</span> <span class="n" style="color: #333;">s</span> <span class="p">(</span><span class="mi" style="color: #099;">1343394373</span><span class="p">,</span> <span class="mi" style="color: #099;">2334675641764441681</span><span class="p">,</span> <span class="mi" style="color: #099;">8462090425404900981</span><span class="p">,</span> <span class="mi" style="color: #099;">7309377810959239186</span><span class="p">,</span> <span class="mi" style="color: #099;">2334956330900738055</span><span class="p">,</span> <span class="mi" style="color: #099;">7234312004409924891</span><span class="p">,</span> <span class="mi" style="color: #099;">7598538378327304247</span><span class="p">,</span> <span class="mi" style="color: #099;">2506435</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/* => "Size of neighbourhood peforming ungapped extension" */</span><span class="p">;</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_UNGAP_SCORE_THRESHOLD</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ObsfucatedString</span> <span class="n" style="color: #333;">s</span> <span class="p">(</span><span class="mi" style="color: #099;">1343394373</span><span class="p">,</span> <span class="mi" style="color: #099;">7234312004410632535</span><span class="p">,</span> <span class="mi" style="color: #099;">8027793215337748283</span><span class="p">,</span> <span class="mi" style="color: #099;">7451040048802563084</span><span class="p">,</span> <span class="mi" style="color: #099;">7020393977047239940</span><span class="p">,</span> <span class="mi" style="color: #099;">7309465758872215298</span><span class="p">,</span> <span class="mi" style="color: #099;">8317697112708115827</span><span class="p">,</span> <span class="mi" style="color: #099;">4734917</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/* => "Ungapped threshold trigger a small gapped extension" */</span><span class="p">;</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_SMALLGAP_THRESHOLD</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ObsfucatedString</span> <span class="n" style="color: #333;">s</span> <span class="p">(</span><span class="mi" style="color: #099;">1343394373</span><span class="p">,</span> <span class="mi" style="color: #099;">7813578723338776438</span><span class="p">,</span> <span class="mi" style="color: #099;">7886683048323908479</span><span class="p">,</span> <span class="mi" style="color: #099;">8102082825191820289</span><span class="p">,</span> <span class="mi" style="color: #099;">7954892377262480132</span><span class="p">,</span> <span class="mi" style="color: #099;">1849334301</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/* => "threshold for small gapped extension" */</span><span class="p">;</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_SMALLGAP_BAND_WITH</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ObsfucatedString</span> <span class="n" style="color: #333;">s</span> <span class="p">(</span><span class="mi" style="color: #099;">1343394373</span><span class="p">,</span> <span class="mi" style="color: #099;">7526756838746121824</span><span class="p">,</span> <span class="mi" style="color: #099;">7020393977337103675</span><span class="p">,</span> <span class="mi" style="color: #099;">7309465758865951756</span><span class="p">,</span> <span class="mi" style="color: #099;">8317697112711372549</span><span class="p">,</span> <span class="mi" style="color: #099;">3906567</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/* => "bandwith for small gapped extension" */</span><span class="p">;</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_SMALLGAP_BAND_WITH</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ObsfucatedString</span> <span class="n" style="color: #333;">s</span> <span class="p">(</span><span class="mi" style="color: #099;">1343394373</span><span class="p">,</span> <span class="mi" style="color: #099;">7526756838746121824</span><span class="p">,</span> <span class="mi" style="color: #099;">7020393977337103675</span><span class="p">,</span> <span class="mi" style="color: #099;">7309465758865951756</span><span class="p">,</span> <span class="mi" style="color: #099;">8317697112711372549</span><span class="p">,</span> <span class="mi" style="color: #099;">3906567</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/* => "bandwi<span class="idiff left right">d</span>th for small gapped extension" */</span><span class="p">;</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="131" 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">
131
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<td class="diff-line-num new_line" data-linenumber="131" 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">
131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_NB_PROCESSORS</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ObsfucatedString</span> <span class="n" style="color: #333;">s</span> <span class="p">(</span><span class="mi" style="color: #099;">1343394373</span><span class="p">,</span> <span class="mi" style="color: #099;">8007525917229806156</span><span class="p">,</span> <span class="mi" style="color: #099;">8315161617321362301</span><span class="p">,</span> <span class="mi" style="color: #099;">2337214414350192403</span><span class="p">,</span> <span class="mi" style="color: #099;">7621652</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/* => "Number of processors to use" */</span><span class="p">;</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="132" 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">
132
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<td class="diff-line-num new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_OPEN_GAP_COST</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ObsfucatedString</span> <span class="n" style="color: #333;">s</span> <span class="p">(</span><span class="mi" style="color: #099;">1343394373</span><span class="p">,</span> <span class="mi" style="color: #099;">2337214414365222977</span><span class="p">,</span> <span class="mi" style="color: #099;">7431046177081152372</span><span class="p">,</span> <span class="mi" style="color: #099;">3543041</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/* => "Cost to open a gap" */</span><span class="p">;</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="133" 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">
133
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<td class="diff-line-num new_line" data-linenumber="133" 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">
133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_EXTEND_GAP_COST</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ObsfucatedString</span> <span class="n" style="color: #333;">s</span> <span class="p">(</span><span class="mi" style="color: #099;">1343394373</span><span class="p">,</span> <span class="mi" style="color: #099;">2337214414365222977</span><span class="p">,</span> <span class="mi" style="color: #099;">6998704246243941246</span><span class="p">,</span> <span class="mi" style="color: #099;">1884751680</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/* => "Cost to extend a gap" */</span><span class="p">;</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="312" 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="312" 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">@@ -312,7 +312,7 @@ public:</td>
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<td class="diff-line-num old_line" data-linenumber="312" 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">
312
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<td class="diff-line-num new_line" data-linenumber="312" 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">
312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_UNGAP_NEIGHBOUR_LENGTH</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Size of neighbourhood peforming ungapped extension"</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="313" 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">
313
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<td class="diff-line-num new_line" data-linenumber="313" 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">
313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_UNGAP_SCORE_THRESHOLD</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Ungapped threshold trigger a small gapped extension"</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="314" 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">
314
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<td class="diff-line-num new_line" data-linenumber="314" 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">
314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_SMALLGAP_THRESHOLD</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"threshold for small gapped extension"</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="315" 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">
315
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<td class="diff-line-num new_line old" data-linenumber="315" 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="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_SMALLGAP_BAND_WITH</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"bandwith for small gapped extension"</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="316" 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="315" 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">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_SMALLGAP_BAND_WITH</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"bandwi<span class="idiff left right">d</span>th for small gapped extension"</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="316" 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">
316
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<td class="diff-line-num new_line" data-linenumber="316" 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">
316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_NB_PROCESSORS</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Number of processors to use"</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="317" 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">
317
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<td class="diff-line-num new_line" data-linenumber="317" 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">
317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_OPEN_GAP_COST</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Cost to open a gap"</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="318" 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">
318
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<td class="diff-line-num new_line" data-linenumber="318" 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">
318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m_STR_HELP_EXTEND_GAP_COST</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Cost to extend a gap"</span><span class="p">;</span> <span class="p">}</span></span>
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<li id="2e1c407e5dc580aace165b8cea11b4ac9736dd3d">
<a href="https://salsa.debian.org/med-team/plast/commit/044166896682adeae5f87fd888ea023032fee6eb#2e1c407e5dc580aace165b8cea11b4ac9736dd3d"><strong>src/misc/api/version.hpp</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" 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">@@ -31,7 +31,7 @@ namespace misc {</td>
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31
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define PLAST_NAME "plast"</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** Version of the library. */</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;">#define PLAST_VERSION "<span class="idiff left right">V2.3.0</span>"</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;">#define PLAST_VERSION "<span class="idiff left right">unstable-master</span>"</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="cm" style="color: #998; font-style: italic;">/** Date of the library. */</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define PLAST_BUILD_DATE "xxxx-xx-xx"</span></span>
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<li id="6dffb965ac5862061255c6ea5b3b5cef6ce34546">
<a href="https://salsa.debian.org/med-team/plast/commit/044166896682adeae5f87fd888ea023032fee6eb#6dffb965ac5862061255c6ea5b3b5cef6ce34546"><strong>src/tools/PlastCmd.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="104" 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="104" 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">@@ -104,6 +104,7 @@ using namespace launcher::core;</td>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"><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;">PlastOptionsParser</span> <span class="n" style="color: #333;">parser</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">retcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** We create a Properties instance for collecting both init properties file and user command line options. */</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">IProperties</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">props</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Properties</span> <span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="148" 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">@@ -147,20 +148,23 @@ int main (int argc, char* argv[])</td>
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147
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">OptionFailure</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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148
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">saw</span><span class="p">(</span><span class="n" style="color: #333;">STR_OPTION_HELP</span><span class="p">))</span> <span class="p">{</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">displayHelp</span> <span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span> <span class="p">}</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">displayErrors</span> <span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">displayHelpShort</span><span class="p">();}</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">displayErrors</span> <span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">displayHelpShort</span><span class="p">();</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">retcode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">;</span>}</span></span>
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="152" 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">
152
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<td class="diff-line-num new_line" data-linenumber="153" 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">
153
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">statistics</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GlobalParametersFailure</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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153
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<td class="diff-line-num new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="154" 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">
154
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<td class="diff-line-num new_line" data-linenumber="155" 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">
155
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span> <span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="n" style="color: #333;">MSG_MAIN_MSG2</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">getMessage</span><span class="p">());</span></span>
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<td class="diff-line-num new old_line" data-linenumber="155" 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="156" 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">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">retcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
</pre>
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155
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<td class="diff-line-num new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="156" 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">
156
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<td class="diff-line-num new_line" data-linenumber="158" 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">
158
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">e</span><span class="p">)</span></span>
</pre>
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157
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<td class="diff-line-num new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="158" 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">
158
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<td class="diff-line-num new_line" data-linenumber="160" 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">
160
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span> <span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="n" style="color: #333;">MSG_MAIN_MSG3</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="159" 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="161" 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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">retcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="159" 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">
159
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<td class="diff-line-num new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="160" 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">
160
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<td class="diff-line-num new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(...)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="161" 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">
161
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<td class="diff-line-num new_line" data-linenumber="164" 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">
164
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="162" 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">
162
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<td class="diff-line-num new_line old" data-linenumber="165" 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="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span> <span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="n" style="color: #333;">MSG_MAIN_MSG4</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span> <span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">MSG_MAIN_MSG4</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="163" 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="166" 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">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">retcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
</pre>
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163
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<td class="diff-line-num new_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="164" 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">
164
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<td class="diff-line-num new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="165" 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">
165
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<td class="diff-line-num new_line old" data-linenumber="169" 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="LC165" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="166" 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="169" 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">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">retcode</span></span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="166" 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">
166
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<td class="diff-line-num new_line" data-linenumber="170" 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">
170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"><span class="p">}</span></span></pre>
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