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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/spoa">Debian Med / spoa</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/spoa/-/commit/1b25f09fe49245631f50acd06dfc9b645f016f8f">1b25f09f</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-01T14:13:26+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.0.5+ds</pre>
</li>
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<h4>13 changed files:</h4>
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
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<li class="file-stats">
<a href="#7131a0f90a08bd29c4474f8cff08d3d4a1c36c54">
include/spoa/alignment_engine.hpp
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<li class="file-stats">
<a href="#fc34f7802c8e4e1d8f77ea7adcee918dd50c2131">
include/spoa/graph.hpp
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<li class="file-stats">
<a href="#0e61f2dfddba824cbd5ec69f94eb6bc89754cf67">
src/alignment_engine.cpp
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<li class="file-stats">
<a href="#5b11ed83019dc2479735a42da7b6c9eeb7155c33">
src/graph.cpp
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<li class="file-stats">
<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">
src/main.cpp
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<li class="file-stats">
<a href="#bcc714a60da7848e0bbf581eaf430d24415bf737">
src/simd_alignment_engine.hpp
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<li class="file-stats">
<a href="#5f67d7c88f93758c667ec0cd960232f654001db4">
src/simd_alignment_engine_implementation.hpp
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<li class="file-stats">
<a href="#ca731de7b3d4a672cfab4f02150bee9b9ac0b332">
src/sisd_alignment_engine.cpp
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<li class="file-stats">
<a href="#2f21018c2eed8bc70f064c1f507e49a9ff90fcae">
src/sisd_alignment_engine.hpp
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<li class="file-stats">
<a href="#5d8002bb01150320b7c31fff5e53952e12c00f35">
<span class="deleted-file">
−
test/data/sample.fastq
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<li class="file-stats">
<a href="#912ef3ab91864c7b2095bf7475ab110c2554566d">
<span class="new-file">
+
test/data/sample.fastq.gz
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<li class="file-stats">
<a href="#e0905733f1ea3e757408dba2978d6a92696dcd11">
test/spoa_test.cpp
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<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/spoa/-/commit/1b25f09fe49245631f50acd06dfc9b645f016f8f#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_minimum_required</span><span class="p">(</span>VERSION 3.9<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>spoa VERSION 4.0.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>spoa VERSION 4.0.<span class="idiff left right">5</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">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"> LANGUAGES CXX</span>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cmake"> DESCRIPTION <span class="s2" style="color: #d14;">"Spoa is a c++ library (and tool) for SIMD vectorized partial order alignment."</span><span class="p">)</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cmake"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,7 +61,7 @@ target_include_directories(${PROJECT_NAME} PUBLIC</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cmake"> cereal<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>BUILD_SHARED_LIBS<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set_property</span><span class="p">(</span>TARGET <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span> PROPERTY SOVERSION = <span class="s2" style="color: #d14;">"<span class="idiff left right">5</span>.0.0"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set_property</span><span class="p">(</span>TARGET <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span> PROPERTY SOVERSION = <span class="s2" style="color: #d14;">"<span class="idiff left right">7</span>.0.0"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>spoa_generate_dispatch<span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -77,6 +77,8 @@ if (spoa_generate_dispatch)</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cmake"> $<BUILD_INTERFACE:<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/include></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cmake"> $<BUILD_INTERFACE:<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/vendor/simde></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cmake"> $<INSTALL_INTERFACE:include><span class="p">)</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>_<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">arch</span><span class="si" style="color: #d14;">}</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cmake"> cereal<span class="p">)</span></span>
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80
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set_target_properties</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>_<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">arch</span><span class="si" style="color: #d14;">}</span> PROPERTIES</span>
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81
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cmake"> COMPILE_FLAGS <span class="s2" style="color: #d14;">"-m</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">arch</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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82
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>BUILD_SHARED_LIBS<span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -132,6 +134,9 @@ endif ()</td>
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132
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>spoa_build_tests <span class="s2" style="color: #d14;">"Build spoa unit tests"</span> OFF<span class="p">)</span></span>
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133
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>spoa_build_tests<span class="p">)</span></span>
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134
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>GTest REQUIRED<span class="p">)</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET biosoup<span class="p">)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL<span class="p">)</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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135
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET bioparser<span class="p">)</span></span>
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136
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>vendor/bioparser EXCLUDE_FROM_ALL<span class="p">)</span></span>
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137
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</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">@@ -144,5 +149,5 @@ if (spoa_build_tests)</td>
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144
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cmake"> biosoup</span>
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145
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cmake"> GTest::Main<span class="p">)</span></span>
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146
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>_test PRIVATE</span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cmake"> SPOA_DATA_PATH=<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/test/data/sample.fastq"</span><span class="p">)</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cmake"> SPOA_DATA_PATH=<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/test/data/sample.fastq<span class="idiff left right">.gz</span>"</span><span class="p">)</span></span>
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148
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span></pre>
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<li id="7131a0f90a08bd29c4474f8cff08d3d4a1c36c54">
<a href="https://salsa.debian.org/med-team/spoa/-/commit/1b25f09fe49245631f50acd06dfc9b645f016f8f#7131a0f90a08bd29c4474f8cff08d3d4a1c36c54"><strong>include/spoa/alignment_engine.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">@@ -56,7 +56,7 @@ class AlignmentEngine {</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Prealloc</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">)</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="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">8</span>_t</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">)</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="LC60" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">Align</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sequence</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">@@ -66,7 +66,7 @@ class AlignmentEngine {</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">Align</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <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;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">)</span> <span class="k" style="font-weight: 600;"><span class="idiff left">noexcept</span></span><span class="idiff right"> </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="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">)</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="LC70" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="nl">protected:</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentEngine</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">@@ -79,6 +79,10 @@ class AlignmentEngine {</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span> <span class="n" style="color: #333;">q</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">WorstCaseAlignmentScore</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">graph_len</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentType</span> <span class="n" style="color: #333;">type_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentSubtype</span> <span class="n" style="color: #333;">subtype_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span> <span class="n" style="color: #333;">m_</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/spoa/-/commit/1b25f09fe49245631f50acd06dfc9b645f016f8f#fc34f7802c8e4e1d8f77ea7adcee918dd50c2131"><strong>include/spoa/graph.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">@@ -292,7 +292,8 @@ class Graph {</td>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC293" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ExtractSubgraph</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">begin</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC295" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">InitializeMultipleSequenceAlignment</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC295" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">InitializeMultipleSequenceAlignment</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">row_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">num_codes_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC299" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">coder_</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/spoa/-/commit/1b25f09fe49245631f50acd06dfc9b645f016f8f#0e61f2dfddba824cbd5ec69f94eb6bc89754cf67"><strong>src/alignment_engine.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -98,4 +98,15 @@ Alignment AlignmentEngine::Align(</td>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">sequence</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">AlignmentEngine</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">WorstCaseAlignmentScore</span><span class="p">(</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">i</span><span class="p">,</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">gap_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="p">]</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="p">{</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">g_</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">len</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="n" style="color: #333;">e_</span><span class="p">,</span> <span class="n" style="color: #333;">q_</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">len</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="n" style="color: #333;">c_</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="p">};</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">m_</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gap_score</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">abs</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;">j</span><span class="p">))),</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">gap_score</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gap_score</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace spoa</span></span></pre>
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<li id="5b11ed83019dc2479735a42da7b6c9eeb7155c33">
<a href="https://salsa.debian.org/med-team/spoa/-/commit/1b25f09fe49245631f50acd06dfc9b645f016f8f#5b11ed83019dc2479735a42da7b6c9eeb7155c33"><strong>src/graph.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -318,9 +318,11 @@ bool Graph::IsTopologicallySorted() const {</td>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC321" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InitializeMultipleSequenceAlignment</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC321" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InitializeMultipleSequenceAlignment</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">row_size</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC323" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">dst</span><span class="p">(</span><span class="n" style="color: #333;">nodes_</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_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;">j</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;">rank_to_node_</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;">i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">j</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="LC325" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_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;">rank_to_node_</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;">i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rank_to_node_</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">dst</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">jt</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">aligned_nodes</span><span class="p">)</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">@@ -328,16 +330,20 @@ std::vector<std::uint32_t> Graph::InitializeMultipleSequenceAlignment() const {</td>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">row_size</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">row_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dst</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC339" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GenerateMultipleSequenceAlignment</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">include_consensus</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">node_id_to_column</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">InitializeMultipleSequenceAlignment</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">row_size</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="LC342" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">node_id_to_column</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">InitializeMultipleSequenceAlignment</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">row_size</span><span class="p">);</span></span>
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337
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"></span>
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338
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<pre style="margin: 0;"> <span id="LC344" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">dst</span><span class="p">;</span></span>
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339
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_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;">sequences_</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;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC340" 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;">row</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">node_id_to_column</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">);</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" 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;">row</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">row_size</span></span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">);</span></span>
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341
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequences_</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">node_id_to_column</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decoder_</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">code</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">@@ -349,7 +355,7 @@ std::vector<std::string> Graph::GenerateMultipleSequenceAlignment(</td>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">include_consensus</span><span class="p">)</span> <span class="p">{</span></span>
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">TraverseHeaviestBundle</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC352" 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;">row</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">node_id_to_column</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC358" 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;">row</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">row_size</span></span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">);</span></span>
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353
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">consensus_</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">node_id_to_column</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decoder_</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">code</span><span class="p">];</span></span>
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,6 @@ std::unique_ptr<bioparser::Parser<biosoup::Sequence>> CreateParser(</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="n" style="color: #333;">str</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="n" style="color: #333;">str</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;">suff</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">suff</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">suff</span><span class="p">)</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="LC32" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fasta"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fasta.gz"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fna"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fna.gz"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".faa"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".faa.gz"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -263,18 +262,35 @@ int main(int argc, char** argv) {</td>
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263
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sequences</span><span class="p">)</span> <span class="p">{</span></span>
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"> <span class="n" style="color: #333;">max_sequence_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> <span class="p">}</span></span>
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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;">alignment_engine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Prealloc</span><span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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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;">alignment_engine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Prealloc</span><span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">exception</span><span class="p">)</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">exception</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="p">}</span></span>
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267
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"></span>
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268
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Graph</span> <span class="n" style="color: #333;">graph</span><span class="p">{};</span></span>
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269
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273
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<pre style="margin: 0;"> <span id="LC273" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">is_reversed</span><span class="p">;</span></span>
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270
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sequences</span><span class="p">)</span> <span class="p">{</span></span>
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271
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">score</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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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignment_engine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">alignment</span><span class="p">;</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignment_engine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">exception</span><span class="p">)</span> <span class="p">{</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">exception</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="p">}</span></span>
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273
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"></span>
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274
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_strand_ambiguous</span><span class="p">)</span> <span class="p">{</span></span>
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275
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ReverseAndComplement</span><span class="p">();</span></span>
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276
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">score_rev</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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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">alignment_rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignment_engine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">score_rev</span><span class="p">);</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">alignment_rev</span><span class="p">;</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" 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="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">alignment_rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignment_engine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">score_rev</span><span class="p">);</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">exception</span><span class="p">)</span> <span class="p">{</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">exception</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="p">}</span></span>
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278
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">score_rev</span><span class="p">)</span> <span class="p">{</span></span>
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279
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ReverseAndComplement</span><span class="p">();</span></span>
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">is_reversed</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -285,7 +301,11 @@ int main(int argc, char** argv) {</td>
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC303" 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="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">AddAlignment</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quality</span><span class="p">);</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quality</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">AddAlignment</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">);</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">AddAlignment</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quality</span><span class="p">);</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"> <span class="p">}</span></span>
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289
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">exception</span><span class="p">)</span> <span class="p">{</span></span>
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290
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310
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<pre style="margin: 0;"> <span id="LC310" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">exception</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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291
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</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">@@ -48,12 +48,12 @@ class SimdAlignmentEngine: public AlignmentEngine {</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Prealloc</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">)</span> <span class="k" style="font-weight: 600;">override</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">8</span>_t</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">)</span> <span class="k" style="font-weight: 600;">override</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">Align</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"> <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;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;"><span class="idiff left">noexcept</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">override</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">override</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">friend</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AlignmentEngine</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">CreateSimdAlignmentEngine</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentType</span> <span class="n" style="color: #333;">type</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">@@ -78,34 +78,34 @@ class SimdAlignmentEngine: public AlignmentEngine {</td>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">T</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">Linear</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">T</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">Affine</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">T</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">Convex</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">num_codes</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">8</span>_t</span> <span class="n" style="color: #333;">num_codes</span><span class="p">);</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">T</span><span class="p">></span></span>
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103
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Initialize</span><span class="p">(</span></span>
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104
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <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;">sequence</span><span class="p">,</span></span>
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105
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">normal_matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">normal_matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">Implementation</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;"> <span id="LC111" 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;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Implementation</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pimpl_</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/spoa/-/commit/1b25f09fe49245631f50acd06dfc9b645f016f8f#5f67d7c88f93758c667ec0cd960232f654001db4"><strong>src/simd_alignment_engine_implementation.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">@@ -6,9 +6,11 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "simd_alignment_engine.hpp"</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cmath></span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits></span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <memory></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdexcept></span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="s" style="color: #d14;">"C"</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">@@ -47,8 +49,8 @@ inline void* align(</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Architecture</span> <span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">T</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">AllocateAlignedMemory</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">storage</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint32</span>_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint32</span>_t</span> <span class="n" style="color: #333;">alignment</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">size</span>_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">size</span>_t</span> <span class="n" style="color: #333;">alignment</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">storage</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">T</span><span class="p">[</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alignment</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">storage</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">storage_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alignment</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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="311" 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -311,12 +313,12 @@ struct SimdAlignmentEngine<A>::Implementation {</td>
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<pre style="margin: 0;"> <span id="LC313" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">node_id_to_rank</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC315" 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;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">__mxxxi</span><span class="p">[]</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sequence_profile_storage</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">sequence_profile_size</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">sequence_profile_size</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">__mxxxi</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sequence_profile</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC319" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">first_column</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC320" 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;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">__mxxxi</span><span class="p">[]</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">M_storage</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">M_size</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">M_size</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">__mxxxi</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">H</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"> <span class="n" style="color: #333;">__mxxxi</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">F</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">__mxxxi</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -371,34 +373,50 @@ SimdAlignmentEngine<A>::SimdAlignmentEngine(</td>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Architecture</span> <span class="n" style="color: #333;">A</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SimdAlignmentEngine</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Prealloc</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(__AVX2__) || defined(__SSE4_1__) || defined(USE_SIMDE)</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">longest_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_sequence_len</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">alphabet_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="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="cpp"> <span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[spoa::SimdAlignmentEngine::Prealloc] error: too large sequence!"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_penalty</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC380" 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;">max</span><span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">m_</span><span class="p">),</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">n_</span><span class="p">)),</span></span>
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<pre style="margin: 0;">-<span id="LC381" 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;">max</span><span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">g_</span><span class="p">),</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">q_</span><span class="p">)));</span></span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(__AVX2__) || defined(__SSE4_1__) || defined(USE_SIMDE)</span></span>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_penalty</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">longest_path</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="cpp"> <span class="n" style="color: #333;">alphabet_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="cpp"> <span class="n" style="color: #333;">alphabet_size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">worst_case_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WorstCaseAlignmentScore</span><span class="p">(</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">);</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">worst_case_score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">min</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="p">{</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">worst_case_score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">min</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">,</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">alphabet_size</span><span class="p">);</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bad_alloc</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ba</span><span class="p">)</span> <span class="p">{</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[spoa::SimdAlignmentEngine::Prealloc] error: insufficient memory!"</span><span class="p">);</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"> <span class="p">}</span></span>
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388
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="389" 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">
389
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<td class="diff-line-num new_line old" data-linenumber="401" 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="LC389" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span></span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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391
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<td class="diff-line-num new_line old" data-linenumber="401" 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="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">alphabet_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sequence_len</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="392" 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">
392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">alphabet_size</span><span class="p">);</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="403" 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">
403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="404" 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">
404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="n" style="color: #333;">alphabet_size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bad_alloc</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ba</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[spoa::SimdAlignmentEngine::Prealloc] error: insufficient memory!"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="p">}</span></span>
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"></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;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Architecture</span> <span class="n" style="color: #333;">A</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SimdAlignmentEngine</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Realloc</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">num_codes</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">8</span>_t</span> <span class="n" style="color: #333;">num_codes</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(__AVX2__) || defined(__SSE4_1__) || defined(USE_SIMDE)</span></span>
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403
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421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">node_id_to_rank</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;">matrix_height</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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422
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="cpp"> <span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">node_id_to_rank</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">matrix_height</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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">@@ -489,9 +507,9 @@ template<Architecture A> template<typename T></td>
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SimdAlignmentEngine</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Initialize</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="cpp"> <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;">sequence</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">normal_matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">normal_matrix_width</span><span class="p">,</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(__AVX2__) || defined(__SSE4_1__) || defined(USE_SIMDE)</span></span>
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">padding_penatly</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC515" 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;">max</span><span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">m_</span><span class="p">),</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">n_</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">@@ -666,54 +684,90 @@ template<Architecture A></td>
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684
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="cpp"><span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">SimdAlignmentEngine</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Align</span><span class="p">(</span></span>
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685
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="cpp"> <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;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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686
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">())</span> <span class="p">{</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[spoa::SimdAlignmentEngine::Align] error: too large sequence!"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Alignment</span><span class="p">();</span></span>
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695
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="cpp"> <span class="p">}</span></span>
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696
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(__AVX2__) || defined(__SSE4_1__) || defined(USE_SIMDE)</span></span>
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">longest_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="cpp"> <span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">;</span></span>
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698
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_penalty</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">m_</span><span class="p">),</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">n_</span><span class="p">)),</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">g_</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">worst_case_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WorstCaseAlignmentScore</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="cpp"> <span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="cpp"></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">worst_case_score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">min</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="p">{</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[spoa::SimdAlignmentEngine::Align] error: possible overflow!"</span><span class="p">);</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">worst_case_score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">min</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" 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;">ceil</span><span class="p">(</span><span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">sequence_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">num_codes</span><span class="p">());</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bad_alloc</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ba</span><span class="p">)</span> <span class="p">{</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[spoa::SimdAlignmentEngine::Align] error: insufficient memory!"</span><span class="p">);</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp"> <span class="p">}</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="cpp"> <span class="n" style="color: #333;">Initialize</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">>></span><span class="p">(</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp"> <span class="n" style="color: #333;">sequence</span><span class="p">,</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="cpp"> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="720" 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">
720
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<pre style="margin: 0;">+<span id="LC720" 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;">ceil</span><span class="p">(</span><span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">sequence_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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<td class="diff-line-num new new_line" data-linenumber="721" 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">
721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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679
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="680" 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">
680
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<td class="diff-line-num new_line old" data-linenumber="723" 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="LC680" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_penalty</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">longest_path</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">())</span> <span class="p">{</span></span>
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681
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<td class="diff-line-num new_line" data-linenumber="723" 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">
723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subtype_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentSubtype</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kLinear</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="682" 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">
682
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<td class="diff-line-num new_line old" data-linenumber="724" 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="LC682" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Linear</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">16_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Linear</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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683
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725
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subtype_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentSubtype</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kAffine</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="684" 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">
684
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Affine</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">16_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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<td class="diff-line-num new new_line" data-linenumber="726" 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">
726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Affine</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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685
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727
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subtype_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentSubtype</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kConvex</span><span class="p">)</span> <span class="p">{</span></span>
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686
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<pre style="margin: 0;">-<span id="LC686" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Convex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">16_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Convex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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687
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729
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<pre style="margin: 0;"> <span id="LC729" class="line" lang="cpp"> <span class="p">}</span></span>
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688
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730
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<pre style="margin: 0;"> <span id="LC730" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="731" 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">
731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="733" 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">
733
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<pre style="margin: 0;">+<span id="LC733" 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;">ceil</span><span class="p">(</span><span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">sequence_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">num_codes</span><span class="p">());</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bad_alloc</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ba</span><span class="p">)</span> <span class="p">{</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[spoa::SimdAlignmentEngine::Align] error: insufficient memory!"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="cpp"> <span class="p">}</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="cpp"> <span class="n" style="color: #333;">Initialize</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">>></span><span class="p">(</span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="cpp"> <span class="n" style="color: #333;">sequence</span><span class="p">,</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="cpp"> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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744
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<pre style="margin: 0;">+<span id="LC744" 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;">ceil</span><span class="p">(</span><span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">sequence_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="cpp"></span>
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689
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747
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subtype_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentSubtype</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kLinear</span><span class="p">)</span> <span class="p">{</span></span>
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690
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Linear</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Linear</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">16_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subtype_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentSubtype</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kAffine</span><span class="p">)</span> <span class="p">{</span></span>
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692
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Affine</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Affine</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">16_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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693
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subtype_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentSubtype</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kConvex</span><span class="p">)</span> <span class="p">{</span></span>
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694
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Convex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Convex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">InstructionSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">16_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Alignment</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Architecture</span> <span class="n" style="color: #333;">A</span><span class="p">></span> <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">T</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="cpp"><span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">SimdAlignmentEngine</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Linear</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(__AVX2__) || defined(__SSE4_1__) || defined(USE_SIMDE)</span></span>
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">normal_matrix_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">matrix_width</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span></span>
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">))</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">matrix_height</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">normal_matrix_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">;</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">matrix_width</span> <span class="o" style="font-weight: 600;">=</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" 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;">ceil</span><span class="p">(</span><span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">sequence_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">);</span></span>
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712
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769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rank_to_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">rank_to_node</span><span class="p">();</span></span>
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713
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="cpp"></span>
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714
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span><span class="n" style="color: #333;">matrix_width</span><span class="p">,</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">num_codes</span><span class="p">());</span></span>
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715
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="cpp"> <span class="n" style="color: #333;">Initialize</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">normal_matrix_width</span><span class="p">,</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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716
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="cpp"></span>
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">type</span> <span class="n" style="color: #333;">kNegativeInfinity</span> <span class="o" style="font-weight: 600;">=</span></span>
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718
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772
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<pre style="margin: 0;"> <span id="LC772" 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;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">type</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">min</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -759,7 +813,7 @@ Alignment SimdAlignmentEngine<A>::Linear(</td>
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759
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813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_set1_epi</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first_column</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span><span class="p">]),</span></span>
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760
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kRSS</span><span class="p">);</span></span>
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761
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815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="cpp"></span>
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762
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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763
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817
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// get diagonal</span></span>
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764
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818
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="cpp"> <span class="n" style="color: #333;">__mxxxi</span> <span class="n" style="color: #333;">t1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mmxxx_srli_si</span><span class="p">(</span><span class="n" style="color: #333;">H_pred_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kRSS</span><span class="p">);</span></span>
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765
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819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="cpp"> <span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mmxxx_or_si</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">@@ -782,7 +836,7 @@ Alignment SimdAlignmentEngine<A>::Linear(</td>
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782
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836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_set1_epi</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first_column</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span><span class="p">]),</span></span>
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783
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837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kRSS</span><span class="p">);</span></span>
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784
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838
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="cpp"></span>
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785
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<pre style="margin: 0;">-<span id="LC785" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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786
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840
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// get diagonal</span></span>
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787
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841
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="cpp"> <span class="n" style="color: #333;">__mxxxi</span> <span class="n" style="color: #333;">t1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mmxxx_srli_si</span><span class="p">(</span><span class="n" style="color: #333;">H_pred_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kRSS</span><span class="p">);</span></span>
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788
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842
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="cpp"> <span class="n" style="color: #333;">__mxxxi</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mmxxx_or_si</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -806,7 +860,7 @@ Alignment SimdAlignmentEngine<A>::Linear(</td>
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806
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860
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="cpp"> <span class="n" style="color: #333;">g</span><span class="p">),</span></span>
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807
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861
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kRSS</span><span class="p">);</span></span>
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862
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="cpp"></span>
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809
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<pre style="margin: 0;">-<span id="LC809" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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810
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864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// add last element of previous vector into this one</span></span>
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811
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865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="cpp"> <span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_max_epi</span><span class="p">(</span></span>
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812
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866
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="cpp"> <span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="851" 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="905" 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">@@ -851,14 +905,13 @@ Alignment SimdAlignmentEngine<A>::Linear(</td>
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851
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905
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<pre style="margin: 0;"> <span id="LC905" class="line" lang="cpp"> <span class="p">}</span></span>
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852
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906
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<pre style="margin: 0;"> <span id="LC906" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">max_j</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Alignment</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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912
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<pre style="margin: 0;"> <span id="LC912" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_score</span><span class="p">;</span></span>
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856
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913
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<pre style="margin: 0;"> <span id="LC913" class="line" lang="cpp"> <span class="p">}</span></span>
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857
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914
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<pre style="margin: 0;"> <span id="LC914" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC858" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">max_j</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// no alignment found</span></span>
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<pre style="margin: 0;">-<span id="LC859" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Alignment</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC860" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC915" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">)</span> <span class="p">{</span></span>
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916
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<pre style="margin: 0;"> <span id="LC916" class="line" lang="cpp"> <span class="n" style="color: #333;">max_j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mmxxx_index_of</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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917
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<pre style="margin: 0;"> <span id="LC917" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">H</span><span class="p">[</span><span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix_width</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">@@ -1057,20 +1110,15 @@ Alignment SimdAlignmentEngine<A>::Linear(</td>
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1110
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<pre style="margin: 0;"> <span id="LC1110" class="line" lang="cpp"></span>
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1058
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1111
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<pre style="margin: 0;"> <span id="LC1111" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Architecture</span> <span class="n" style="color: #333;">A</span><span class="p">></span> <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">T</span><span class="p">></span></span>
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1112
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<pre style="margin: 0;"> <span id="LC1112" class="line" lang="cpp"><span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">SimdAlignmentEngine</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Affine</span><span class="p">(</span></span>
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1060
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<pre style="margin: 0;">-<span id="LC1060" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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1061
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1114
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<pre style="margin: 0;"> <span id="LC1114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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1062
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1115
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span> <span class="p">{</span></span>
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1063
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(__AVX2__) || defined(__SSE4_1__) || defined(USE_SIMDE)</span></span>
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1064
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<pre style="margin: 0;">-<span id="LC1064" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">normal_matrix_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">;</span></span>
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1065
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<pre style="margin: 0;">-<span id="LC1065" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">matrix_width</span> <span class="o" style="font-weight: 600;">=</span></span>
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1066
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<td class="diff-line-num new_line old" data-linenumber="1117" 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="LC1066" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span></span>
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1067
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<td class="diff-line-num new_line old" data-linenumber="1117" 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="LC1067" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">))</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1068" 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">
1068
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<td class="diff-line-num new_line old" data-linenumber="1117" 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="LC1068" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">matrix_height</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">normal_matrix_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">;</span></span>
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1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">matrix_width</span> <span class="o" style="font-weight: 600;">=</span></span>
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1119
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<pre style="margin: 0;">+<span id="LC1119" 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;">ceil</span><span class="p">(</span><span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">sequence_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">);</span></span>
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1069
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1120
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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rank_to_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">rank_to_node</span><span class="p">();</span></span>
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1070
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1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="cpp"></span>
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1071
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<td class="diff-line-num new_line old" data-linenumber="1122" 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="LC1071" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span><span class="n" style="color: #333;">matrix_width</span><span class="p">,</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">num_codes</span><span class="p">());</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1072" 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">
1072
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<td class="diff-line-num new_line old" data-linenumber="1122" 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="LC1072" class="line" lang="cpp"> <span class="n" style="color: #333;">Initialize</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">normal_matrix_width</span><span class="p">,</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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1073
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<pre style="margin: 0;">-<span id="LC1073" class="line" lang="cpp"></span>
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1074
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<td class="diff-line-num new_line" data-linenumber="1122" 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">
1122
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<pre style="margin: 0;"> <span id="LC1122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">type</span> <span class="n" style="color: #333;">kNegativeInfinity</span> <span class="o" style="font-weight: 600;">=</span></span>
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1075
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<td class="diff-line-num new_line" data-linenumber="1123" 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">
1123
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<pre style="margin: 0;"> <span id="LC1123" 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;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">type</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">min</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>
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1076
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1124
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<pre style="margin: 0;"> <span id="LC1124" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1169" 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">@@ -1121,7 +1169,7 @@ Alignment SimdAlignmentEngine<A>::Affine(</td>
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1121
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1169
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<pre style="margin: 0;"> <span id="LC1169" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_set1_epi</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first_column</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span><span class="p">]),</span></span>
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1122
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1170
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<pre style="margin: 0;"> <span id="LC1170" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kRSS</span><span class="p">);</span></span>
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1123
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1171
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<pre style="margin: 0;"> <span id="LC1171" class="line" lang="cpp"></span>
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1124
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<pre style="margin: 0;">-<span id="LC1124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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1172
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<pre style="margin: 0;">+<span id="LC1172" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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1125
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1173
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<pre style="margin: 0;"> <span id="LC1173" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// update F</span></span>
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1126
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1174
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<pre style="margin: 0;"> <span id="LC1174" class="line" lang="cpp"> <span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_add_epi</span><span class="p">(</span></span>
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1127
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1175
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<pre style="margin: 0;"> <span id="LC1175" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_max_epi</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1148" 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="1196" 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">@@ -1148,7 +1196,7 @@ Alignment SimdAlignmentEngine<A>::Affine(</td>
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1148
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1196
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<pre style="margin: 0;"> <span id="LC1196" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_set1_epi</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first_column</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span><span class="p">]),</span></span>
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1149
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1197
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<pre style="margin: 0;"> <span id="LC1197" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kRSS</span><span class="p">);</span></span>
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1150
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1198
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<pre style="margin: 0;"> <span id="LC1198" class="line" lang="cpp"></span>
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1151
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<pre style="margin: 0;">-<span id="LC1151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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1199
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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1152
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1200
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<pre style="margin: 0;"> <span id="LC1200" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// update F</span></span>
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1153
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1201
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<pre style="margin: 0;"> <span id="LC1201" class="line" lang="cpp"> <span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_max_epi</span><span class="p">(</span></span>
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1154
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1202
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="cpp"> <span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1174" 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="1222" 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">@@ -1174,7 +1222,7 @@ Alignment SimdAlignmentEngine<A>::Affine(</td>
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1174
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1222
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<pre style="margin: 0;"> <span id="LC1222" class="line" lang="cpp"> <span class="n" style="color: #333;">__mxxxi</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">zeroes</span><span class="p">;</span></span>
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1175
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1223
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<pre style="margin: 0;"> <span id="LC1223" class="line" lang="cpp"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_set1_epi</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first_column</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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1176
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1224
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<pre style="margin: 0;"> <span id="LC1224" class="line" lang="cpp"></span>
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1177
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<pre style="margin: 0;">-<span id="LC1177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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1225
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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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1178
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<td class="diff-line-num new_line" data-linenumber="1226" 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">
1226
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<pre style="margin: 0;"> <span id="LC1226" class="line" lang="cpp"> <span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_max_epi</span><span class="p">(</span><span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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1179
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1227
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<pre style="margin: 0;"> <span id="LC1227" class="line" lang="cpp"></span>
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1180
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1228
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<pre style="margin: 0;"> <span id="LC1228" class="line" lang="cpp"> <span class="n" style="color: #333;">E_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_add_epi</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1225" 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="1273" 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">@@ -1225,14 +1273,13 @@ Alignment SimdAlignmentEngine<A>::Affine(</td>
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1225
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1273
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<pre style="margin: 0;"> <span id="LC1273" class="line" lang="cpp"> <span class="p">}</span></span>
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1226
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1274
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<pre style="margin: 0;"> <span id="LC1274" class="line" lang="cpp"> <span class="p">}</span></span>
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1227
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1275
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<pre style="margin: 0;"> <span id="LC1275" class="line" lang="cpp"></span>
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<td class="diff-line-num new old_line" data-linenumber="1228" 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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1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">max_j</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Alignment</span><span class="p">();</span></span>
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1278
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="cpp"> <span class="p">}</span></span>
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1228
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1279
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1229" 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">
1229
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1280
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<pre style="margin: 0;"> <span id="LC1280" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_score</span><span class="p">;</span></span>
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1230
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1281
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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="cpp"> <span class="p">}</span></span>
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1231
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1282
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<pre style="margin: 0;"> <span id="LC1282" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="1232" 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">
1232
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<td class="diff-line-num new_line old" data-linenumber="1283" 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="LC1232" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">max_j</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// no alignment found</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1233" 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">
1233
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<pre style="margin: 0;">-<span id="LC1233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Alignment</span><span class="p">();</span></span>
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1234
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<pre style="margin: 0;">-<span id="LC1234" class="line" lang="cpp"> <span class="p">}</span></span>
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1235
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<pre style="margin: 0;">-<span id="LC1235" class="line" lang="cpp"></span>
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1236
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1283
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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">)</span> <span class="p">{</span></span>
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1237
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1284
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<pre style="margin: 0;"> <span id="LC1284" class="line" lang="cpp"> <span class="n" style="color: #333;">max_j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mmxxx_index_of</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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1238
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1285
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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">H</span><span class="p">[</span><span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix_width</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">@@ -1510,20 +1557,16 @@ Alignment SimdAlignmentEngine<A>::Affine(</td>
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1557
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<pre style="margin: 0;"> <span id="LC1557" class="line" lang="cpp"></span>
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1558
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<pre style="margin: 0;"> <span id="LC1558" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Architecture</span> <span class="n" style="color: #333;">A</span><span class="p">></span> <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">T</span><span class="p">></span></span>
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1512
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1559
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<pre style="margin: 0;"> <span id="LC1559" class="line" lang="cpp"><span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">SimdAlignmentEngine</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Convex</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC1513" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1560" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1561" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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1562
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<pre style="margin: 0;"> <span id="LC1562" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span> <span class="p">{</span></span>
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1516
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1563
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<pre style="margin: 0;"> <span id="LC1563" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(__AVX2__) || defined(__SSE4_1__) || defined(USE_SIMDE)</span></span>
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<pre style="margin: 0;">-<span id="LC1517" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">normal_matrix_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1518" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">matrix_width</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">-<span id="LC1519" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span></span>
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<pre style="margin: 0;">-<span id="LC1520" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">))</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1521" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">matrix_height</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1564
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<pre style="margin: 0;">+<span id="LC1564" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">normal_matrix_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1565" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">matrix_width</span> <span class="o" style="font-weight: 600;">=</span></span>
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1566
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<pre style="margin: 0;">+<span id="LC1566" 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;">ceil</span><span class="p">(</span><span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">sequence_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNumVar</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1567" 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">
1567
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<pre style="margin: 0;">+<span id="LC1567" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">matrix_height</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1522
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<td class="diff-line-num new_line" data-linenumber="1568" 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">
1568
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<pre style="margin: 0;"> <span id="LC1568" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rank_to_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">rank_to_node</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="1523" 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">
1523
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1569
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<pre style="margin: 0;"> <span id="LC1569" class="line" lang="cpp"></span>
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1524
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<td class="diff-line-num new_line old" data-linenumber="1570" 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="LC1524" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span><span class="n" style="color: #333;">matrix_width</span><span class="p">,</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">num_codes</span><span class="p">());</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1525" 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">
1525
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<td class="diff-line-num new_line old" data-linenumber="1570" 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="LC1525" class="line" lang="cpp"> <span class="n" style="color: #333;">Initialize</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">normal_matrix_width</span><span class="p">,</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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1526
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<pre style="margin: 0;">-<span id="LC1526" class="line" lang="cpp"></span>
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1527
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1570
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<pre style="margin: 0;"> <span id="LC1570" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">type</span> <span class="n" style="color: #333;">kNegativeInfinity</span> <span class="o" style="font-weight: 600;">=</span></span>
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1528
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1571
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<pre style="margin: 0;"> <span id="LC1571" 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;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">type</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">min</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>
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1529
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1572
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<pre style="margin: 0;"> <span id="LC1572" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1584" 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="1627" 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">@@ -1584,7 +1627,7 @@ Alignment SimdAlignmentEngine<A>::Convex(</td>
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1584
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1627
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<pre style="margin: 0;"> <span id="LC1627" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_set1_epi</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first_column</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span><span class="p">]),</span></span>
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1585
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<td class="diff-line-num new_line" data-linenumber="1628" 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">
1628
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<pre style="margin: 0;"> <span id="LC1628" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kRSS</span><span class="p">);</span></span>
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1586
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<td class="diff-line-num new_line" data-linenumber="1629" 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">
1629
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<pre style="margin: 0;"> <span id="LC1629" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="1587" 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">
1587
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<td class="diff-line-num new_line old" data-linenumber="1630" 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="LC1587" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1588" 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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1630
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<pre style="margin: 0;">+<span id="LC1630" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1588" 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">
1588
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<td class="diff-line-num new_line" data-linenumber="1631" 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">
1631
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<pre style="margin: 0;"> <span id="LC1631" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// update F</span></span>
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<td class="diff-line-num old_line" data-linenumber="1589" 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">
1589
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<td class="diff-line-num new_line" data-linenumber="1632" 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">
1632
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<pre style="margin: 0;"> <span id="LC1632" class="line" lang="cpp"> <span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_add_epi</span><span class="p">(</span></span>
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<td class="diff-line-num old_line" data-linenumber="1590" 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">
1590
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<td class="diff-line-num new_line" data-linenumber="1633" 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">
1633
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<pre style="margin: 0;"> <span id="LC1633" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_max_epi</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1662" 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">@@ -1619,7 +1662,7 @@ Alignment SimdAlignmentEngine<A>::Convex(</td>
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1619
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1662
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<pre style="margin: 0;"> <span id="LC1662" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_set1_epi</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first_column</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span><span class="p">]),</span></span>
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1620
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1663
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<pre style="margin: 0;"> <span id="LC1663" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kRSS</span><span class="p">);</span></span>
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1621
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1664
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<pre style="margin: 0;"> <span id="LC1664" class="line" lang="cpp"></span>
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1622
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<pre style="margin: 0;">-<span id="LC1622" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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1665
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<pre style="margin: 0;">+<span id="LC1665" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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1623
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1666
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<pre style="margin: 0;"> <span id="LC1666" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// update F</span></span>
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1624
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1667
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<pre style="margin: 0;"> <span id="LC1667" class="line" lang="cpp"> <span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_max_epi</span><span class="p">(</span></span>
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1625
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1668
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<pre style="margin: 0;"> <span id="LC1668" class="line" lang="cpp"> <span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1659" 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="1702" 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">@@ -1659,7 +1702,7 @@ Alignment SimdAlignmentEngine<A>::Convex(</td>
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1659
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1702
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<pre style="margin: 0;"> <span id="LC1702" class="line" lang="cpp"></span>
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1660
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1703
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<pre style="margin: 0;"> <span id="LC1703" class="line" lang="cpp"> <span class="n" style="color: #333;">__mxxxi</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">zeroes</span><span class="p">;</span></span>
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1661
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1704
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<pre style="margin: 0;"> <span id="LC1704" class="line" lang="cpp"></span>
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1662
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<pre style="margin: 0;">-<span id="LC1662" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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1705
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<pre style="margin: 0;">+<span id="LC1705" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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1663
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1706
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<pre style="margin: 0;"> <span id="LC1706" class="line" lang="cpp"> <span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_max_epi</span><span class="p">(</span></span>
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1664
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1707
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<pre style="margin: 0;"> <span id="LC1707" class="line" lang="cpp"> <span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span></span>
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1665
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1708
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<pre style="margin: 0;"> <span id="LC1708" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mmxxx_max_epi</span><span class="p">(</span><span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">O_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1729" 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="1772" 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">@@ -1729,14 +1772,13 @@ Alignment SimdAlignmentEngine<A>::Convex(</td>
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1729
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1772
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<pre style="margin: 0;"> <span id="LC1772" class="line" lang="cpp"> <span class="p">}</span></span>
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1730
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1773
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<pre style="margin: 0;"> <span id="LC1773" class="line" lang="cpp"> <span class="p">}</span></span>
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1731
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1774
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<pre style="margin: 0;"> <span id="LC1774" class="line" lang="cpp"></span>
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1775
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<pre style="margin: 0;">+<span id="LC1775" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">max_j</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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1776
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<pre style="margin: 0;">+<span id="LC1776" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Alignment</span><span class="p">();</span></span>
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1777
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<pre style="margin: 0;">+<span id="LC1777" class="line" lang="cpp"> <span class="p">}</span></span>
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1732
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1778
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<pre style="margin: 0;"> <span id="LC1778" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1733" 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">
1733
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<td class="diff-line-num new_line" data-linenumber="1779" 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">
1779
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<pre style="margin: 0;"> <span id="LC1779" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_score</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1734" 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">
1734
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1780
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<pre style="margin: 0;"> <span id="LC1780" class="line" lang="cpp"> <span class="p">}</span></span>
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1735
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<td class="diff-line-num new_line" data-linenumber="1781" 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">
1781
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<pre style="margin: 0;"> <span id="LC1781" class="line" lang="cpp"></span>
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1736
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<pre style="margin: 0;">-<span id="LC1736" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">max_j</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// no alignment found</span></span>
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1737
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<pre style="margin: 0;">-<span id="LC1737" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Alignment</span><span class="p">();</span></span>
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1738
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<pre style="margin: 0;">-<span id="LC1738" class="line" lang="cpp"> <span class="p">}</span></span>
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1739
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<pre style="margin: 0;">-<span id="LC1739" class="line" lang="cpp"></span>
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1740
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1782
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<pre style="margin: 0;"> <span id="LC1782" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">)</span> <span class="p">{</span></span>
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1741
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<td class="diff-line-num new_line" data-linenumber="1783" 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">
1783
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<pre style="margin: 0;"> <span id="LC1783" class="line" lang="cpp"> <span class="n" style="color: #333;">max_j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mmxxx_index_of</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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1742
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<td class="diff-line-num new_line" data-linenumber="1784" 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">
1784
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<pre style="margin: 0;"> <span id="LC1784" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">H</span><span class="p">[</span><span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">]),</span></span>
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<li id="ca731de7b3d4a672cfab4f02150bee9b9ac0b332">
<a href="https://salsa.debian.org/med-team/spoa/-/commit/1b25f09fe49245631f50acd06dfc9b645f016f8f#ca731de7b3d4a672cfab4f02150bee9b9ac0b332"><strong>src/sisd_alignment_engine.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,6 +4,7 @@</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits></span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdexcept></span></span>
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7
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"></span>
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8
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "spoa/graph.hpp"</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,14 +63,26 @@ SisdAlignmentEngine::SisdAlignmentEngine(</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SisdAlignmentEngine</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Prealloc</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[spoa::SisdAlignmentEngine::Prealloc] error: too large sequence!"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">max_sequence_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alphabet_size</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">alphabet_size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bad_alloc</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ba</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[spoa::SisdAlignmentEngine::Prealloc] error: insufficient memory!"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SisdAlignmentEngine</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Realloc</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">num_codes</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">8</span>_t</span> <span class="n" style="color: #333;">num_codes</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">node_id_to_rank</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;">matrix_height</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">node_id_to_rank</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">matrix_height</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -243,35 +256,49 @@ void SisdAlignmentEngine::Initialize(</td>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"><span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">SisdAlignmentEngine</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Align</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"> <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;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[spoa::SisdAlignmentEngine::Align] error: too large sequence!"</span><span class="p">);</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="p">}</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"></span>
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247
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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248
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Alignment</span><span class="p">();</span></span>
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249
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="p">}</span></span>
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250
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">WorstCaseAlignmentScore</span><span class="p">(</span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</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;">kNegativeInfinity</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[spoa::SisdAlignmentEngine::Align] error: possible overflow!"</span><span class="p">);</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="p">}</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span><span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">num_codes</span><span class="p">());</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bad_alloc</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ba</span><span class="p">)</span> <span class="p">{</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[spoa::SisdAlignmentEngine::Align] error: insufficient memory!"</span><span class="p">);</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="280" 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">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">Initialize</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">);</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"></span>
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251
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<td class="diff-line-num new_line" data-linenumber="282" 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">
282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subtype_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentSubtype</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kLinear</span><span class="p">)</span> <span class="p">{</span></span>
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252
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<td class="diff-line-num new_line old" data-linenumber="283" 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="LC252" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Linear</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">sequence</span>_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Linear</span><span class="p">(</span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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253
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subtype_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentSubtype</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kAffine</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Affine</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">sequence</span>_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Affine</span><span class="p">(</span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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255
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subtype_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentSubtype</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kConvex</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Convex</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">sequence</span>_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Convex</span><span class="p">(</span><span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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257
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"> <span class="p">}</span></span>
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258
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Alignment</span><span class="p">();</span></span>
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259
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"><span class="p">}</span></span>
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260
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"></span>
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261
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"><span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">SisdAlignmentEngine</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Linear</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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263
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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264
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span> <span class="p">{</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">matrix_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">matrix_height</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">matrix_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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267
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rank_to_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">rank_to_node</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC298" 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;">Realloc</span><span class="p">(</span><span class="n" style="color: #333;">matrix_width</span><span class="p">,</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">num_codes</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="cpp"> <span class="n" style="color: #333;">Initialize</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><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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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">max_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">type_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">kNegativeInfinity</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_i</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 right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_j</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 right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">update_max_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_score</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_j</span><span class="p">]</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">H_row</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -297,7 +324,7 @@ Alignment SisdAlignmentEngine::Linear(</td>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">H_pred_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">H</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// update H</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"> <span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span></span>
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302
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">H_pred_row</span><span class="p">[</span><span class="n" style="color: #333;">j</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="n" style="color: #333;">char_profile</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span></span>
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303
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">H_pred_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">g_</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">@@ -308,7 +335,7 @@ Alignment SisdAlignmentEngine::Linear(</td>
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308
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335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"></span>
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309
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336
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="n" style="color: #333;">H_pred_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">H</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">]);</span></span>
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310
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337
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"></span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">H_pred_row</span><span class="p">[</span><span class="n" style="color: #333;">j</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="n" style="color: #333;">char_profile</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC341" 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;">max</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">@@ -317,7 +344,7 @@ Alignment SisdAlignmentEngine::Linear(</td>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"> <span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</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="n" style="color: #333;">g_</span><span class="p">,</span> <span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">)</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">@@ -332,6 +359,9 @@ Alignment SisdAlignmentEngine::Linear(</td>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="cpp"> <span class="p">}</span></span>
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">max_j</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Alignment</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -430,19 +460,15 @@ Alignment SisdAlignmentEngine::Linear(</td>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="cpp"><span class="p">}</span></span>
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461
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="cpp"><span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">SisdAlignmentEngine</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Affine</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">matrix_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">matrix_height</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">matrix_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rank_to_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">rank_to_node</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span><span class="n" style="color: #333;">matrix_width</span><span class="p">,</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">num_codes</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="cpp"> <span class="n" style="color: #333;">Initialize</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">max_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">type_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">kNegativeInfinity</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_i</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 right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_j</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 right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">update_max_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_score</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_j</span><span class="p">]</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">H_row</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</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">@@ -471,7 +497,7 @@ Alignment SisdAlignmentEngine::Affine(</td>
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">F_pred_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">F</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// update F and H</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="cpp"> <span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="cpp"> <span class="n" style="color: #333;">H_pred_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">g_</span><span class="p">,</span></span>
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="cpp"> <span class="n" style="color: #333;">F_pred_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -484,7 +510,7 @@ Alignment SisdAlignmentEngine::Affine(</td>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="cpp"> <span class="n" style="color: #333;">H_pred_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">H</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">]);</span></span>
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511
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="cpp"> <span class="n" style="color: #333;">F_pred_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">F</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="cpp"> <span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="cpp"> <span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC516" 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;">max</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">@@ -498,7 +524,7 @@ Alignment SisdAlignmentEngine::Affine(</td>
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// update E and H</span></span>
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">E_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">E</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;">matrix_width</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="cpp"> <span class="n" style="color: #333;">E_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</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="n" style="color: #333;">g_</span><span class="p">,</span> <span class="n" style="color: #333;">E_row</span><span class="p">[</span><span class="n" style="color: #333;">j</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="n" style="color: #333;">e_</span><span class="p">);</span></span>
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529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="cpp"> <span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">E_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]));</span></span>
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530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -514,6 +540,9 @@ Alignment SisdAlignmentEngine::Affine(</td>
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">max_j</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Alignment</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -647,19 +676,15 @@ Alignment SisdAlignmentEngine::Affine(</td>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="cpp"><span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">SisdAlignmentEngine</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Convex</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">matrix_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">matrix_height</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">matrix_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rank_to_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">rank_to_node</span><span class="p">();</span></span>
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684
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="cpp"> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span><span class="n" style="color: #333;">matrix_width</span><span class="p">,</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">num_codes</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="cpp"> <span class="n" style="color: #333;">Initialize</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">max_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">type_</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">kNegativeInfinity</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_i</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 right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_j</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 right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">update_max_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_score</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_j</span><span class="p">]</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">H_row</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</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">@@ -691,7 +716,7 @@ Alignment SisdAlignmentEngine::Convex(</td>
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">O_pred_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">O</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="cpp"></span>
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// update F, O and H</span></span>
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694
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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695
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="cpp"> <span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">H_pred_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">g_</span><span class="p">,</span> <span class="n" style="color: #333;">F_pred_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</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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696
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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="cpp"> <span class="n" style="color: #333;">O_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">H_pred_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q_</span><span class="p">,</span> <span class="n" style="color: #333;">O_pred_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">c_</span><span class="p">);</span></span>
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697
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="cpp"> <span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H_pred_row</span><span class="p">[</span><span class="n" style="color: #333;">j</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="n" style="color: #333;">char_profile</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="704" 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="729" 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">@@ -704,7 +729,7 @@ Alignment SisdAlignmentEngine::Convex(</td>
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704
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729
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<pre style="margin: 0;"> <span id="LC729" class="line" lang="cpp"> <span class="n" style="color: #333;">F_pred_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">F</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">]);</span></span>
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705
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730
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<pre style="margin: 0;"> <span id="LC730" class="line" lang="cpp"> <span class="n" style="color: #333;">O_pred_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">O</span><span class="p">[</span><span class="n" style="color: #333;">pred_i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">]);</span></span>
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706
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731
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="cpp"></span>
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707
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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708
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733
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="cpp"> <span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span></span>
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709
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734
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="cpp"> <span class="n" style="color: #333;">F_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span></span>
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710
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735
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<pre style="margin: 0;"> <span id="LC735" 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;">max</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="722" 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="747" 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">@@ -722,7 +747,7 @@ Alignment SisdAlignmentEngine::Convex(</td>
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722
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747
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// update E, Q and H</span></span>
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723
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748
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">E_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">E</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;">matrix_width</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Q_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pimpl_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Q</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;">matrix_width</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="cpp"> <span class="n" style="color: #333;">E_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</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="n" style="color: #333;">g_</span><span class="p">,</span> <span class="n" style="color: #333;">E_row</span><span class="p">[</span><span class="n" style="color: #333;">j</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="n" style="color: #333;">e_</span><span class="p">);</span></span>
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752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="cpp"> <span class="n" style="color: #333;">Q_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</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="n" style="color: #333;">q_</span><span class="p">,</span> <span class="n" style="color: #333;">Q_row</span><span class="p">[</span><span class="n" style="color: #333;">j</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="n" style="color: #333;">c_</span><span class="p">);</span></span>
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753
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="cpp"> <span class="n" style="color: #333;">H_row</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -743,6 +768,9 @@ Alignment SisdAlignmentEngine::Convex(</td>
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768
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="cpp"> <span class="p">}</span></span>
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">max_j</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Alignment</span><span class="p">();</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="cpp"> <span class="p">}</span></span>
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774
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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747
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775
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_score</span><span class="p">;</span></span>
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748
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776
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/spoa/-/commit/1b25f09fe49245631f50acd06dfc9b645f016f8f#2f21018c2eed8bc70f064c1f507e49a9ff90fcae"><strong>src/sisd_alignment_engine.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">@@ -34,12 +34,12 @@ class SisdAlignmentEngine: public AlignmentEngine {</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Prealloc</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">)</span> <span class="k" style="font-weight: 600;">override</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">8</span>_t</span> <span class="n" style="color: #333;">alphabet_size</span><span class="p">)</span> <span class="k" style="font-weight: 600;">override</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">Align</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;"><span class="idiff left">noexcept</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">override</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">override</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="nl">private:</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">SisdAlignmentEngine</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">@@ -53,24 +53,24 @@ class SisdAlignmentEngine: public AlignmentEngine {</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">Linear</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">Affine</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">Convex</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">graph</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">noexcept</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Realloc</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">num_codes</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">matrix_width</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">matrix_height</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">8</span>_t</span> <span class="n" style="color: #333;">num_codes</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Initialize</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <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;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sequence_len</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/spoa/-/commit/1b25f09fe49245631f50acd06dfc9b645f016f8f#5d8002bb01150320b7c31fff5e53952e12c00f35"><strong>test/data/sample.fastq</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">@0</span>
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<td class="diff-line-num old old_line" data-linenumber="2" 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">
2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">GTCTAATGCGCTTTGTTGGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAAACGGTTTTTCCATGACAGGAGTTGAATATGGCATTCCGTAATCCCTCGTCGATGATCCAAGCGGGAGCGGTCTAAGTATTGCGCATATGCGCAGGGATTCAGTCTTGCGCCGCAAACAATGCGGTCTTGTACGCTCCGGCAGGCTGGGACATTGTGTCAGCCGCAGTCCACAGGCGTCCTGCCAGCAGTGGCTGGAGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTACCCAGGTTTGCAGGAGGGCACAATGAGCCAGCATTTACCTCGGCTTCTGCCGCACAGCCCGGCATCTCATCGTAAGCAGAAAAACTGTCAGAATTACCCTCCCCCTGGCTCGCCATGTGCGCATTACGTTGAGTTAACCGCGAGGAGAGGTTGATTCACCCACTTGAGCCCGCGCGGTGGTTGCCTGTACACAGCCCACGGCAGGATACAC</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">+</span>
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<td class="diff-line-num old old_line" data-linenumber="4" 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">
4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</span>
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<td class="diff-line-num old old_line" data-linenumber="5" 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">
5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">@1</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">ATGATGCGCTTTGTGTTGGCGCGGTGGCTTACATCTGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACAAGGATTGAATATGGCATTCAGTAATCCCTTCGATGATCGCAGGGAGCGTTAGTCGATATTGCGCCACAATGCGCAGGAGCGTAATTCAGTCTGTGGCCGCAACAAGCGTGGCGTCTTACCGGCAGGGCTGGGACATTGTGTGTCGACCGCAGCTTTACAGGCGGTTGGGTCGGAGCAGTGGCTGGAAGCCCACTGGGGGTCAACTCTGACACCGACTGAAGTTTTACCCGATTCAGGAGAGGCACAATGAGCCAGCAAGTTTACCTGTTATGTGCCCGCACAGCCACAGGCATCTGGATGGCAGAAAAACTGTCAGAATTACTAGCCGCTGCGGAGCGTGGGCGCATCTCCTCGTTGAGTTAACCGCCAGAGTTGACTTCACATTACTGGCCCGCGCGGTGGTCCGCCGACTACGCAATAGCAGATACGC</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">+</span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">/0/./1000/1-0-0...-...--..-..-.-,,/,----.-//--../..----.,,-,,-..,.--++-,,-,,-,,--+++,/.,-..//-...-.-.------+,-.,,,,---,.--..,-+,.,-,-1//.//,+.,,,/-/,-,,,,++++0.,-,/,+-,,.+,,+*,++,,++-,,-*,++**+***+++,**),**+)*,+,+,**)*,))),)*++,*)++)**,),*)*+((+),))+**++*,+****)))+))+*)-+*,+*++*+**-***++**)*,,++-+-,,*,*++*+++*-+++,,*,-.+,,,-+++*++/++,.++,,,./-,,+-,+,+,----/,.,-.-./..-.-,+,.,,,,,.--/----,++,.--,-,++-,--.,,---,-.-,-++++,++-+-,+,,+**-+++*+*-+++,++****-*,+++*,,+**++****+*++*)****+***,++,*,+,,+-+++,,,+,,.,,</span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">@2</span>
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<td class="diff-line-num old old_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">GATCCTCAGGTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAAACCACTTTTCCATGACAGGAGTTAGAATATGGCATTCAGTAATCCCTTCGGCCGGATGATCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTACCCAGTGCAGGGAGGCACAATGAGCCAGCATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGGATGGCAGAAAACTGTCAGAATTACCCTCCGCCTGGAGCTGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACACTGGCCCGCGCGGTGGTTATGCCGGACTAGCGCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">+</span>
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<td class="diff-line-num old old_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">-+.+-+--+-.-,-,.+,,,,++,+++*,++,/+,+,,,++,+,,,,+-,-,+,++,,+,,+*,+*****,++,+0-+0/,+++-++.,-,-.+++,+,-,,,,/*-*+*,,,-/,,--------020/1,,../1.0----.-0/..1//.--./.1/00////.1..///.../0/0.2/0/.0.../0/1000/0/..3//3//1//--0-//.//.0/...0/0030/2../-1-./1..1..--,,-,.--/.-///0//./...0.--./-..0.--..,,/.--,-0,--,--...10/0/-//..040/0-/././--/.././.0.1..0.////////10./2//./-0/3000.,,.././/-../--.1..1/.---./--..//-/-.0..0---/-------../.-.,/-.,-/--.---/.-/..1./2//.--/...--00---..-..-/..-,///----0.0</span>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">@3</span>
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<td class="diff-line-num old old_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">ACCTTAATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCATCGACCTCGTAAACCAACACTTTTCCAGATGACAGGAGTTGAATATGGCATTCAGTAATCCCCCTTCTAGATGATCGCAGGGAGCGTTTTACATCTGCGCAATGCGCAGGGGCAATTCAGTCTGGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACATGCGTCCTGTGCCAGCAGTGGCTGGAAGCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTGCTTTGGTCGCCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCACTGGAGCTTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGTCGCCGGACGCTCACGCAAGCAGATTGAGGTC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">-,-..-./0//101..-,,-/-/-.-//./0-,.2-../,0-----1-./..-/0..///./////-.-...-0..0///..-...//-//././0--10.00-11....-//0101--/////..25211..//0-/0.--/./-/,-..--.-..0/1-.//--/---.,.--/...0--/-,-,,,--//./-.--.1/./...-,/,,--.-.0.--,-/0-.0./,-,/....0/0//0/..-/.-/...1...0///////.1./0././010..0.-..0/0.1.-2///.../.50001.00/002/////001..1/10/.././//00./.12//10/-.///0/.0.1./4./--/.//0/--....--.0../..///-..-/0.-.-.0/,..-.+++++.,,,-,-.,/-+,-,+,--,++-,,,++.+++*,+,*)**)*)*),**+++*-,+,+*,,+**,+)***),+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">@4</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGTGGCTTGATGCGCAGGGCTAATCGACCTCTGGCAACCACTTTTCCATGGACAGGAGTTGAATATGGCGGCATTCAGTAATCCCTGTCGCCCATGATCCGCGCAGGGAGCGTTTACATATTTGCGCAATGCGCAGGGGCAGGAGTTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTCAGCCGCAGTCAAGGAGCGTCCTCAGCAGTGGCTGGAAGCCCACTGGCGCGTACTCTGACACCGACGAATTTACCCAGTTGCAGGAGAGGCACAATGGCTCAGCATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTAGACCTCCACCATTCTTGGTCCCGCCTGACCGCAAGCGAATACCAC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="20" 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">
20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">./0-..../00/00..///01//00//....1///0./-.0001/0.2/0/...-..31/300-----/---...,-/-.../..-,-...--.--,-,,--,,-.,/,,,//,,-,,,..--0----,/--,,,-.../.--,,0-,-.-.....-..-./-./.../1..0.-...-0-./...0.-,,-,,,.-...-.-,,+-0..-.-,/-/,-.,/-.--++,,,+.---,+,--/0//0...-----//.1.-./--..--.,-/--../--..012/11/./12302/.///0//0./0/000/0///1200/01//0000//1//0100///.//./////.0//./1//./.0/0000/.-./001/0.././/0..../-.0--,--/2-.-/.--+,,,,,,,+,,+,,.,-,+.+++*,+,-*+*+**-++++,-..+,,+******.++-+.+,,-,,,+++,-++.+-</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">@5</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="22" 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">
22
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">ATGATGCGCTTTGTTGTGCGCGGCTTATGCCGGGAGTGGACCTCTGGCAACCACTTTTCCATGACAGGGTTGAATATGGCATTCAGTAATCCCTTCGGATGATCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTACGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCCAGTGCAGGAGGGCACAATGAGCCAGCATTACCTTTGGTCGCCGCACAGCCCGGCATCTGGCCTGAGAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTAACGTTGAGTTAACCGGAGAGGATGATTGGGCCATTACTGGCCCGCGCGGTGGTGCCAGCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="23" 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">
23
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="24" 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">
24
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">+++++,,,,,--,.+.++,+++,,+++,,++---++,+,/+--..-//--,...-/-,,,-,--,-+-,-,-./../-...-----2..1//./.,/---./--...--,-./430.-../00//--..-../-/-.--,-..-,,.-/./---,--,,.------.,-0---,,-,-.--.--,++0,,,,,,,,,,...-,,+,+-,-.-,,---,-/-,.0--,+++-+++-,,.-----,---,-/.,,+,,-00/0/.,,,,,.--,/----,.+,-,/---/---,,,.--,,----,.,,,-,+.,,,----,,/..,,,,,,,,,++-,.-,.,+++-.,,+***+**,+**++**++++*+*,++**,*++****)*****++******))))),)*++*+++-+,+,+++--,+++,++,+++++-,,.,,+++,-,,</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="25" 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">
25
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">@6</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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</td>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">ATGATGCTATTTGTTGGCGCGGTGGCTTGATGCAGGGCTAATCGACCTCTGAAACCACTTTTCTCAATGACAGGGTCGAATATGGCATTCATCAATCCCTTCATATGATCGCAGGGAGCGTTTTACATATTTCTCACAGATGCGCAGGGGCAATTCAGTCTGTACGCCCAACAAATGCGTCGCAGCGGCAGGCCGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGGTACATGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTACCTTTACCTCGCTAGACACTAAGCATATGGCCTAACCAAAACTGTCAGAATCTAGCGCCTGGCCTACGTGGCGCATTACGTTGAGTCAAGCGCCAGGTTGATTCGCCATTCTGGCCCGGCGGTGTATGCCCGACTAGCGCAAGCAATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="27" 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">
27
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="28" 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">
28
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</td>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">,,0,,-,+-,+,,,+++,-,,,,,-,++,++,-,,,,,+,-,-,,+,.+/+++-+,-,,-,+*,.,//1,.,,,+,+.,---0,,,,+,--+.,,,,-,,,.,,.-/--,--.-/-/.-/-,,,,/.//.--,,,/--..././---.-0--//-/---..--,/,-,,,,-.-/.00,,++.,---./1---,,,-.----..+,+,-,,.,---+--/-.-.-,,++,,----..--.-,,,-.,,-,---,-.-,--/-/--/---,,-,-.,,,-,,+,+,.+++,+++*-*++++++*+*+**+++++*+**)))*))*+*(()))*)()))***)*))*)()((+(+)*)+)*(())))))()***)*)++*)**+,***+,++*+-++**)***,**++**,+,,+-+,.,,,,--,+,++,+++++++,,,++,+***,++++,+,,-,.,.,,-,,</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="29" 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">
29
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">@7</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">GATGCGCTTTGTTGTGGCGCGTGTCGCTTTACGATGCAGGGCTAATCGACCTCTGGCAACCACTTTTCTCATGACAGGAGTTGAATATGATTCTTCAGTAATCCCTTCATATCAATCCGCAGGAGCGTTTTACAGTCCGCGCAGATGCGCAGGGCAATTTCAGTCTGTGGCCGCGCCAACAATGCGTCTCTTACCGGCAGGCTGGGACATTGTGTCAGCCGCAGTCACAGGCGTCTTCAGTATCTTACCCTCGAAGCATTTTTGCGCTACGCAGCGACGAATGATGTATATCCAAGCGTGTTAATAACACCCCAGCATTTCACCTTGTATGCCGCAACACAGCCCGGCATCTGGATGGCAGAAAAGCTGTCAGCGAATCTACTCCGCCTGGAGCCCTCTTTGAATTACGCGTTTATCAGTTGGACCGTTGGTTTTATCAGCGCGGTTGATTCACTTGGTGCGCTAGTTTCTTTACCTGACCGGCGGATAAC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="31" 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">
31
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">/.-/./----./---./...-/,.,,-----//-..2/.-/-,--.--/0/1/0...//0////.//.---...10002/1/1..-331/0-/,//..10//21/.1/./..0./0.01///020020./--0//.1.0-.-.-0.1.0/..///.//./....0/././../.--0,-.//022//---//--.-.././-,,++,.---/,,+,*,,+,,-++,,.,-+.+*,)**))*+)**)*****))**)+**),,*)(,)())+(*(+'((()(()')''&''(('())*,*)('(*'*()*((()+(+*)))))**()))((+)()((+((+*)))(()*))()()()()(*)(***)*)())((+()**))))()***)*****))**+**)**),*)+*,,**))+)**),),))*,-))****+),-.).0**++*+*-+,++*+.**-+-+,++++,,*,+))*-*+*,*,-**,*+*)</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="33" 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">
33
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">@8</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="34" 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">
34
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCAATCGACCTCTGGCAACCACTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCTTCAGCTGATCCAGCGGAGCGTTTTACATATTGCGCAATGCGCAGGAGAATTTCAGTCTGTGGCCGCAACAATGCGTCTTACATGCACAGGCTGGGACATTGTGTCAGCCGCAGTCAGCAGGCGTCCCTGCCAGCAGTGGCTGGAAATCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATTGGCTCTACGATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTCAACCGGAGCGATGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGC</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="35" 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">
35
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="36" 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">
36
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">,,..-./,--...-.-,--/,,-..-,-/--..-,-..--0...../..0..0-.-//0.//.-----/../0/+/,,.---/--------/-..--.--.-..-...--.,-.,,,--,.,++---,/-.,,-,-,--,-.,,++,,,.0-,,,/,+,++,.,/++,----0-,,,.,,,/,--/--.0-,+,-..-.0/-..-....00...0-0..15---..2//01/010011/.-..//1.1/1/01000--./0.-.0/./../-/.//./,..3.-..,,---/.-.--0/--/-,,,+-0.///.--.....,,,,-,,+,-.--.-,,.--,.-/-.---/,+,-02/0..-,,,,,,-++,+,,.,---,--.-,-+,--.,.-/0+++****+**+++*+,**,,-++,+-,,++++,***+-****))+)****)))*,)*+***,*+,--****+*</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="37" 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">
37
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">@9</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="38" 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">
38
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGGTGTAGTCGTGAGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACAGCGAGTTGAAGTGGGATTCAGTAATCCCTTCGATGATCCGCAGGAGCGTTTACATATTGCGCAATGCTAGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTGTCTTACCGGCAGGCTCGGGACATTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGCTGGAAGCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAAGGAGCTAAGACAATCCAGCATTTACCTTCTTACTCCCGCACAGCCAGCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACTAGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGAGCAGATACA</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="39" 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">
39
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">+</span>
</pre>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">,,-+,,,-,,----,,,,-.-,----.---,/+.,+,,,-,+---,,-.----./,+.,./.-/-,+,,+.,-.,.+----+,.,,------,,+--.-,,-,,.,,-,-,,/+,,,-,,-//.,+-,--.,0,.,.-,,*,+-,.-,./,,.-..-,..-,,,.-,.,,,,0..-3-.--,,-,,---.--/-.-.,,-/.--.-,,,,.-.,..-..-/./././/-.../0.///./..0-/...-0...../../0/./2////./0012101/-.,.10...--.-..-0,./--./..-..-/0//1/....0-/.-----0--./...-,,,./0.-.---.----/,./02/1.0-,,,-.----.--.//.0.-----/.--0/...00/.../---.--,-,-,-,.-1...-.-/0/-.-//-...//.///.0/.-/.---/.---.0-.-.--.1/---..</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="41" 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">
41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">@10</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="42" 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="LC42" class="line" lang="plaintext">ACTTATCCGCTTTGTTGGCGCGGATGATGGTGCAGGGGCTTACGACCTCTGGCAACCACTTTCCATGACAGGAGTTAATATGGCATTGAGTAATCCTCGGTTCGATCAGCCGAGGCTAGTTTTACATGCGGATCCGCAGGGGCAATGCGCTTGGTGGCAACAATCGGCGTCTACCGGCAGGCTGGGACATGTGTGTCAGCCGCAGTCACAGTGCTTTCAGCAGGCTGGAAGCCCACTGAGTACTCTGACACCGACGAATTTACCCAGTTGCAGGAGGCTAATGAGCCAGGATGTTGTGGCCTTCTTACCGCACAGCCGGCATCTCATGGCAGAAAAACTGTCACGATGGCTCCGCTGCGGCTCTTAGCATTACGTTAGAGTTAACCGAGGCTTACTTCGCCATTACTGGCCGCCCCTTATGTGCGTACAAGGGCCCAAGCAAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="44" 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">
44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">,,,,,,,+,,,-+++*+,,,+++++++*),+++++**,*,++,+-+-,./,,,-,,.,,,,+,,,+,--.---,,++,---,-----,,,.--.///-0,,.+,,..+.,,-,,-+,,./.,++++,,,,,-,,+,--+-,,+,-.-+/+++++,,+.,,,-,,,,----+++,-,-.-,/---,-1-.-/--./-0-./-1....-..0-..1/-..-//..1////././-.--0.--./0--..-0.,--,.--,,,++-,--..+----,,,+**++,+++,-+++,*.,+++*.++**+-+*)*--+,++,++++**,++*+***,+,+-,+++-*+*,*++**,**,+-++*-++,+++*--++,+,.+*),+-******)++*))),****+)*,****,*+*,*,**+++*+*++)*)*******+****,+*,*++++,+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="45" 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">
45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">@11</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="46" 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="LC46" class="line" lang="plaintext">ATGATGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCCACGTAGACCTCTGGCAACCACTTTTCCATGACAGGAGTCGCAGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCCAATGCGCAGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGGCAGGCTGGGACATTGTGTCAGCCGCATCACAGGCGTGCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTGTTACTCTGACACCGACGAATTTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTACCTTTTGGTCGCCGCACAGCCCGGCAATCGTATCGGCAGAAAAACTGTCAGAATTATAAGCGCCTGGGAAGCGTGGCGCATCGTTGAGTTAACCGGAGAGGTTGATTCTCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="47" 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">
47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="48" 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="LC48" class="line" lang="plaintext">/02/./.-..-.-----.,+,,.-.,.,--..-..-0,/.--,0//.000//.-/-//0./..-0--.-../01////11/0/100//00/0///1/.10000.0../.0/.210//000046101/.0/10//2...//0/-...-//.1.0....20.0/././...//0/.0,-,,,-.----...0/-----001/0/...-/./-./--./---/.,-,--/././/.../..../../..0.//1.-.--.-,--.-/1.1/../.0./.0/.,-.-/..--/-.,-.,-,,.--.,++,,-/-../-/.2.--,-,,---,,,-.,-..,,,+-,+,,+,,,,,,++..10,.+,,-,-/,,++*-.++**++++*,-+,+,*++,,+,/,+,+,--+,,,,,+,+,+.*+,,+-*++,,,+-----,,--,,+,,+,+-,,++.-+,,+.,+,-/+++,,+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">@12</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="50" 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="LC50" class="line" lang="plaintext">ATGATGCGCTTTGTTGAGGGGTGGCTTGATGCAGGGTAGAGACTTACATAGCCTGGCAACCACCTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTCATGGGTCCACATCTAGCAGGGAGCGTTTTAAGTGCCCAATGCGCAGGGGCAATCGGTCTGTGGCCGCAACAAATGCGTCTACCGGCAAGGCTGGGACATTGTGTCATCGCATAAGAAGGCGTCCTTGCCAGCAGTGGCGGGAAGCCCACTGGCGTACTCTGAGACACCGACGAATTTACCCAGTTGCAGGAGGCAAGTGGCTCAGCATTTACCTTGGTCCCTAACACACAGCCCGGCATCGGATGGCAGAAAAACTGTCAGAATTACCCTCGCCTGGAGCGTGGCATTACCGTTGAGTTAACCGCGAGAGTGATGTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="51" 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">
51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="52" 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="LC52" class="line" lang="plaintext">--.0-..0-------,,,.-,,./---/--./--++,,,+.-,,.+,,-,.,,0--++-+-,,,+,+,+,+*.,-+/+,+*+,,+,++----.,+.,--,..,+./,,,++++-,.-,*.,,,,,--.1../,+,,,,,++,,-0.+,-,,,,,,.,,+*-,+-,,,,+.-+,-.-.,.0--,+,,,,,--.-.1,,+,,0./..--,,+/,,/-----,0/21-/-.--./,.-..--/,-,-.-.,.,0----.-,,-.-.1/,,,,...---/+++--+-*,-++*+++++++-+++++,+**+++.-,,,++++,+*,*+*****,+,,,,,,,,,.--,,-,-,,--,,-./1./--..-.--.,.,--,..../0.//0.-/.//./..1/0...0.///0/...///./..--/,-000/1.///.----..-,/.,-,.,-,+.-,-,.-,---,+.,,+,-,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="53" 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">
53
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</td>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">@13</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="54" 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="LC54" class="line" lang="plaintext">ACATGATGCGCTTTGTTGTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGTGGCAACCACTTTTCCATGACAGGAGTTGAATATGGATTCAGTAATCCCTTCGATGATCCGCGCAGGGAGCGTTTTACATATTGCGCAATGCGCGCAGGGGGGATCTTCAGTCTGTGGCCTACGCAACAATGCGTCTTACGGGCAGGCTGGGACACTATTGTGTGTCAGCCGCAGTCACAGGCGTGCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTGTACCCAGTTGCAGGAGGCAATGAGCCAGCATTTACCTTTGGTCGCCGCAACGCCCGGCATCTGGATGGCAGAAAACTGGTACGAATCACCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAAGAGGTTGATTCGCCATTACTGTACCGCGCGGTGGTGCTCCGGACTAGCGCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="55" 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">
55
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</td>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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</td>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">..0-/....-..-...---...-/-,....--0-0....//00-01111101300./..--0.///.1/.-/..--...-////////3/..2./10..//././,.,-,--.--1--0.......23/...,/.0./1.//../-.,,,/--,--++,,-,-+-.-/0.--,+,,++.++++,-1+20,-,*++****-+++-+****,,++-.,--,,++,*-,.,.-,,--..0,/,+,*+++,,,-------,,/--..-/../.1-/,-.-2-./.0..,--,-,-,,,.,..,1-0/.--,-.----,-0-,,.---..//,----,-+-,,-.----0.0--...-0--//./...---001/3./--0-//..-//..1/2//00//00./-..00//01/0./.././00//.-010/...////1./110.0.-..././/0//.20../.-,/-,..----0--.-.././.2./</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="57" 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">
57
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</td>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">@14</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTCCATGACAGGAGTTGAATATGGCAATTCATGTAATCCCCTTCTATTGACTCAGGCATGGAGCGTTTTACATATTGCGCAATGCGCAGGGCAATTCAGTCTGTGGCCCGCAACAATGCTTTGCCTTACCGGCAGGCTGGGACATTGTGTGTTTAGCCGCAGTCCACAGGCGTCCTTGCCAGCAGTGGCTGGAAGCCCACTGGCGTAGTACTGACACCGACGAATTCCCAGTTTGCAGGAGGCACAATCGGCTACAGCATTTACCTTTGGTCCCGCCGCACAGCCCGCGGGCATCTGGATGGCAGAAAAACTTGTCAGAATTTACCCTCCGCCTTCGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="59" 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="LC59" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="60" 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">
60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">/.--,----,--.-,--,,------,,----/,-,-.-+.....//00./.-,-/,...-/.,+,,,+.,,-0+.------.-,,,-,--,+--,+/-.-,++,+++++,-++-..,,-,.,-./--/++-----,,+,+++-,,+,++**++++,,,,.0-,.,,-++.++-.0,//+,.-++,,++++,+.--.-+,+++//..-,,+,++,+.,.+--+++**-,-+--*++++,+,/-//--,--+/-,-,-,---/-.-/,+++,--,,,--0,,----,-.--...-,.,,,,-+--++-,,,.-+*+--+-./..-..2.---.,,+.,.,+,,.,,+*+++*-++++--,+,++,,++,-021,-++,+++-+-++,+-,,--/-,-,----0//.---///..0//--./.1.././-./././//.21//.//01001/1100//3100/./0//..0..-/.-..--....-,.++,-.+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">@15</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="62" 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">
62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">ATGATGCGCTTTGTTGGGGTGCTTATGCCGCAGGGGCTAATCGACTCTGAAGCCACCTTCCATGACAGGAGTTGAATATGGATTCCGAGTAATCCCTTCGATGATCCTAGCAGGGAGCGTTTTACATTGCGCGACTGCGCAGGGGCAATTCAGTCTTACTCCGGCTCTTGACAATGCGTCTTACCGGCAGGCTCGGGACATTGTGTGTCAGCCGCATTACAGCGGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGCGGGGGTCTATACTGACACCGACGAATTTTACCCAGTTGCAGGGAGAGGCACAATGAGCAGCATTTACCTTGTTCTGCTTAAGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCTCCGTGGCGCATTACGTTGAGTTAAACCCGCAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCTGAGACTAGCGCAAGCAGATACA</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="64" 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">
64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">-/0---./---.,,-,-,-/.-,,,/,/-,----//-,-/../0/-.1..-./.,.,,,,--,/-/--...-.1--/0.-..../.-,,/./../..-.--/...--,,0./....../-..,,-/.-.,-++.,-,,/..-,,/-,-,0-,+,/+-+--+.,,.,-+-.++-,+,,,.++-,-,,+.,,-,+,+++,---,+,-,+,,,+,-,..,++-++,+,+.,+,++++,,+--,-,,,-,+,,,,,+,,.+-+++,,,++*,*-+..+-,++.-+**+..+*,+,+--,++++,+++--++,+,,,,+,,,,--.,,--+,+-,++,+-,+,-,,---,-.-./.-.,,.-..,,,,,,1.21.0-,.,,,,.-----....1./////0.....//../0/0/0/0/...1-.----/---//--.-//-.1/-00/-/-..0.-.0/..--,/,+,--,+++,/-,,,,/----.,0-,-..</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="65" 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">
65
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</td>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">@16</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="66" 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">
66
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</td>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGGGTTGGCTTGATGCAGGGCTAATCGACCTCTGGCAGACCATTTTCCATGACAGGAGTTGAATATGAATTCATAGTAATCCCTTCGGATGATCGCAGGGATGTTTTACATATTGCGGGCAATGCGCAAGCGGGGCAATTCGCCAGTCCTGCCGCAACAATGCGTCTTACGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTACCCAGTGCCAAGGAGGCACAATGAGCCAGCATTTACTTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAGAAATTACCCTCCGCCTGCGGAGCGTGGCGCGATTATACGTTGAGTTAACCGGAGGTTACTTCGCCATTACTGGCCCGCGCGCGGTGTATGCCGGACCCGCGACTAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="67" 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">
67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="68" 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">
68
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">//.-/.0.-///--,-,,-.,,,.++-+-+,,+.++-+-*+,,,,,++,+-,+*+*+*+,,*,-)))++*-++**)),)*+)*+*+,**++*,*+,+,,,++++,,)*,++**++,,,++-++)**+,/,,-,-+.-+.,--.,+,-+*+++++*+-++-,,,,-..+,,+*+++-1.-.0,,/,-*++,,,,,-++++-+,-.,-.-,/,,,--,-/,.-,.01-.-.-,--.//,/-./../.---,,,-./,.-.--.-...//0./.00.....00011.--/.-,.----/....,../././-./.0/1012..///.--/--.-/,-..0.0-./1......-./...--0.202100---,,-//-.--,---.-/-/...-,-,/--,-+-.-,,.+,-/--/-,,-+.,,-,,-.+,+,+-,,-,--,-,,-.,/,,/,./-,,-/0,,--/-++.++++++,+++,+++,-+.+,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="69" 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">
69
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</td>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext">@17</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="70" 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">
70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">ATGAACACGCTTTGTGTTGGCGCGGTGGCTTGATGCAGGGGCGATCGACCTTAGGAGCAACCACTTTTCTAAGTGACAGGAGTTGAATATGGCATTTTCAGTAATCCCTTCGTACGAGGGCAGCGTTTACATATTGCGCAATGCGCAGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTCCACTTGTGTGTCAGCCGCAGTCAGGCGTTCTGCCAGCAGTGGCTGGAACTGGCCCACTGGGCGTACTCTGACACCGACGAATTTTACCCAGGTTGCAGGAGGCACAATGAGCCAGCATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAACTGTCAGAATTACCCTCCGCCTGGAGCTGTGGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACAACACGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="71" 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">
71
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="72" 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">
72
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">/1..-..-/00100...--....,-,1.-///--0----,/1-..../-/,.-,,--.../220..-,,,-,,/---.-.--/----------/..-..--2-.020/././-../--././/2/0//0062211/..4//11./0./--.-//.0-.-/-/--..-.///40012../..--,,-.//--,-,--,-.-.----,,-,--/-..---.,.,++,,,,.---+/----,.+.-/.,.,.,/-,,-,--,1,-,..-.,.,,,02/./.,.,---,-.,0---,,---,,--..,-/-/-/-//../../--/.,-,,,--.--.----,-,.---./-----.///..-,,,.1,/.,.,,,,,-.,/-.,,.,/-,,,/..-,-.0.-,,-,-,,,,,-,,,.-,,,-+,,+--,-,,.,,-+-,-,-0-,-/,.-,,,,--,..-0----../-..--/.</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="73" 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">
73
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext">@18</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="74" 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">
74
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</td>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext">AATGATGCGCCGTGTTGGCGCGGTGGCTTGATGCAGGGTAATCGACCTCTGGCAACCACTTTCATGACATAGGAGTTGAATATGCATTCTCAGTAATCCTTCGATGATCCGCAGGGAGCGTTTTACATATGCGCAATGCACTAGGGCAATTCGAGTCTGGGCATTAAAACCAATGCGTCTTAACCGGACCCAGGCTGGACAATGTGTCAATAGGCGAGTTCTAATATAAGAACGAGTTAGTGCCACATAGCAGTGGATGGGAAGGGACTAGGGTGAATCTGGTGACACCGACGAATTTGAGAGTTTGCAGGAGGAGCACAATGAGCCAGCATTTACGTCCTGGTCGCCGCGCACAGCCCGGCATCTGGATGGAAGAAAAACTGTTACGAATTACCTCGACCCCCGCTCCAAGTTAGAGATGCCGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCTCACGGCGGATCAGTCAGCAGATAC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="75" 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">
75
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="76" 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">
76
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext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span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="77" 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">
77
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">@19</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">ATGAATGCGCTTTGTGTTGCGCGGTGGCTTGATGCAGGGCTAATCGACCTCTGGCAACCACTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGAGTGAGCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTAAGCAGGCTGGGACATTGTGTGTCGACCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACACGACGAATTTACCCGATGTCCAGGAGGCACAATCAGCCATTTACCGCTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGTGATTCGCCATTACTGGCCTAGGGGTGGTTGCCGGACTAGCCCCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="80" 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">
80
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</td>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">/.0../000122030.2...//./.10///.1/1.//0/1.002100/202110100015///0.1.//2///2/01.1011101122010113003241113/0003000011001201214/100222312012011100//0..00211/./2--.-----/.-.-/./0.21.-.-..0.-.0--,+0---.,-+,.++*.**--,+,,,-,,.,--,---+-,,.++.++*++*++++++++-.,,,,.,+.,-,--,-+,,,.,,,,+**+*+**-+,*+,,-*----,.-,,+-,,++*+*+,,,-*+++*+,,,,,+,,.---.-.-0.-,,/---,,/----,.-,,,.2//.,-.....1.//1///3/...-./--../0-0----,,/--.,-,-/,-+.,,---,------,,/.,-,+*+,++,.+,+++++,,+-+,+**++,--,+,-+1,,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">@20</span>
</pre>
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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">GTACGAGGCTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTCGCAACCACCTTTCCATGACAGGGAGTTGAATATGGCATTCAGTAATCCTAGTTCGGATGATCCGCAGCGGAGCGTTTTACATATTGCGCATGCGCAGGGGCAGATTCAGTCTGTGGCCCGCAACAATGCGTCTTACCGGCAGTAGATGGGACATTGTGTCCTAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGTGGAAGCCCACTGGCGTACTCTGACAAGGACGAATTTACCCAGTTGCAGGAGGCACAATCAGCCAGCATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATGACTAGCCCGCTGGAGCGTGGCGCATTACGGTCGAGTTAACCGGAGAGGTTGATTCGCTTACTGGCCCGCGCATTGGTCGTAGCCGGACTAGCGCAAGCAGAACAA</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">-+.-,.,.--.-,,/--.-.-1/--.,--0----.0--/../.2---/,/--/-.14/..0--0..//.///...0/-.///.0/.,,.3-./-./0/,,./--1-.0/--,.-,/,/-,--..,-,+,-/-./-,+..--0,-+,++,+++++,/++++-)-**+,**+-++,++-..--+,+***++,.++*)+****/,+++++***-*,,+---+,,+,..-/,++)+++++,+-++-++,.++,,,,,--,,,--/-0./.--0-..10.,--./..//---..0-/-.1..0.-01./-/....0//053/3.-////--/--.--/...0./--/00//.----/-,,--././0//.,/++,-,,.,,+--,-.---,---,+,,,,-,+-+/++,+..,-,,,,+**++-,-,-+-,,,-,.,.++++,+,0++-,,*+,+*-+,++++..+,,+,,-,-,-.*,,+,+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="85" 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">
85
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</td>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext">@21</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">ATGTTGCTTTGTTGTGCGTGGCTTGATGCAGGGGCTAATTAGACCTCTGGCAACCACTTTCTCATGACAGGAGTGAATATGGCATTCAGTAATCCTTCGATGATCCGCAGCCATAGGGGAGCGTTTTACTATCCTAATGCGCAGCGGATTCAGTCTGTGGCCGCAACAATGCGTCTTACGGCAGGCTGGACATTGTGTCCTACAGCCGCATGTCAGGCGTCCTGCCACTGGCTGCTGGAAGCCCGGCGTACTCTGACACTAGACGAATTTTACCCAGTTGCAGGGAGAGCAACGTATGATCTAAGCGTTAGCTGTTATCCCGCAAACAGCCCGGCATCTCAGATGGCAGAAAAACTGTCATAGAATTACCCTCCGCCTGGAGCGTGGCAATTACGTTGGAGTTAACCGGAGAGGTTGATTCGGGGTCTTACTCATCCGCGCGTGGTTGCCGGACTCTAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="87" 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">
87
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</td>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="88" 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">
88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">**())*+)*+***)++)*++.+,+.+,,,***++,*++++**,-++++-++*-+-,-,,,+),*+*+-,+++*--*++++*+)*)*****++,-,,****+*++********+*),****-+6,**+*+*+,++++,-.-+,++-**+++++,-,+*++,+-++++-,/-./,,-*,+.,,-,,,-,,++-,--,-+-+++*,.++-,-,,*-+*+,.,+,+++,*,+,*+,-,+++.++++***+--*)+*-/,+.+,***-+,-,.-,,*,**-,,,,,,,*+++,++*+-,++-,+-+*,.-..,,,,,.,,,*****,+*++-,+++++.-,,,,,*++,*+,,++,.-/,--++++*))**+**+,-,,,,+-,-,,-,+****+,**+,,+*****,****))*))**+++,,+,,*+++++*+,+++*+**+,+++,***,,*****++***++.,+++,,,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="89" 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">
89
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">@22</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="90" 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">
90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">ATGATCCAATTTGTTGGCGCGGTGGCTTGATGCAGGGGCTATAAATCGACCTGGCGGCACCACTTTTCCATGACACAGGGGAGTTGAATATGGATTCAGTAATCCCCTTCGATGATCAAGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTGAAGGCAGGCTGGGACATTGTGTGTCATGAGCCGCAGTCACACCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACAAAGCGACGAATTTTACCCGATCAGTTGCGCAGGGGCACAATCAGCCGAGCATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGATGAGGCAGAAAACGTCAGAATTACCCTCCGCTGGCCGCTACCCTGCGCATTACATTCAGGTTAACCCGGAGGTTGATTCGCCATTACTGGCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATGGGA</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="91" 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">
91
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</td>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="92" 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">
92
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">//-..-..0-////-.../0.0.41../12.0./../01./.0001110/0000/11020342421/020/10020111012/2//031/110122212211220/0/03/13//0/1000000//15141.1../001/00.1/111./..-,.,1-.-.4-0/.-.,,,++-+,,0.--/+.+,+++,++..,,.+,,++,+-.+,-+-+..++++,+,,,,-.-/,,,,,..+..-.,.0-,/,+,++,+,.,+-,+.-.,,-/-----...-----../--10-,++-,++,/,--,+,-0,,,.,-,.,---,,,-+,-1-,/+,,.,-++++++,,+---.,.,-,.-,,0-,+--,*,-,+,-,,,,-+**+,+,*))*)**,+++*++**,)+*+*)+*+++*)****,),*)+)())))**,++**.*+*,*)*+,+*++++++.,,***+,*--,++++++++,,-.--//.--/-,,.</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="93" 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">
93
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">@23</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="94" 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">
94
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">ATGATGCGCTTGTTGGCGCATGGTGGCTTGATGGTGCAGGGGCTAATCGACCTCTGGCAACCACTTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGGATGATCCGCAAGGGAGCGTTTTACATGATGCGCAATGCGCAGGGAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGAGGACATTGTGTGTCAGCCGCAGTCACGCAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTATACTCTGACACCGACGAATTACCCAGTTGCAAGGAGGCACACAATGAGCCAGGATTTTACCTTTGGTCGCCGCACAGCCATCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCGCCTGGAGCGTGGGCGCATTTACGTCAATTAACCGGAGTAGGTTGATTCGCTTACTAACTGCCGCGCGGTGTGGTTTGCCGAGACTAGCGCGACCCATGCC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="95" 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">
95
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="96" 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">
96
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext">/0//1/3.../1/../../.-.-.-.//./-,.-.......0..//00/3.3/10/.//.-23../..--/.///.0/2/.1.//110//.3.0.//.1//01....,/-/0/...-/...//./120//..///1/.//.0/.//0.0./.-../.40.41.././.--.0./20/22/./0...-/.01//0./0-0-2//0/0--0-0--.........--,..,0---,,-.,---20,--/,-,,+,-,+,,,/-/-/-/,,-/--1--.-.-.-.---,-,-,,./,-,,--.--..-0///0//-./...//200.././0...-.--0/./00.31110..02./00....-..,-0-///0/-/,,,.-.-,-/--1.--.-,-,.,,,+,,-../,--,/,/,-,+,-,,,+-,**,,-,+,-+++++*****-+,,+,/-.-.++.,+-.++++++,*-+++,/-,,.,,,.+,,,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="97" 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">
97
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext">@24</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext">GTCTAATGCGCTTTGTTGGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAAACGGTTTTTCCATGACAGGAGTTGAATATGGCATTCCGTAATCCCTCGTCGATGATCCAAGCGGGAGCGGTCTAAGTATTGCGCATATGCGCAGGGATTCAGTCTTGCGCCGCAAACAATGCGGTCTTGTACGCTCCGGCAGGCTGGGACATTGTGTCAGCCGCAGTCCACAGGCGTCCTGCCAGCAGTGGCTGGAGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTACCCAGGTTTGCAGGAGGGCACAATGAGCCAGCATTTACCTCGGCTTCTGCCGCACAGCCCGGCATCTCATCGTAAGCAGAAAAACTGTCAGAATTACCCTCCCCCTGGCTCGCCATGTGCGCATTACGTTGAGTTAACCGCGAGGAGAGGTTGATTCACCCACTTGAGCCCGCGCGGTGGTTGCCTGTACACAGCCCACGGCAGGATACAC</span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="99" 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">
99
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="100" 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">
100
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext">,.+*++/,.,-,--,.+-++,+++-,-+-+++.,*++-,*,,,,+,--.,-,++++..---,,,+++++++.,,,+,.*+**+++*,-,+*,),*+++*+**),**+,+++****+)),),++***+)()+**)+*+*,))*)-+-*+++*-+*+,**+,)+**)*)***+++*,*+,*,-.*,-**++*,,,,+-,,--,,++,---,,-,,,--.---.-,,,-1--,/-+,,,-/-0-//-././.-,..,2..------,-/---,.-,-/----,-,-..///--,-,,,,.,-,,-.--+,,+-.,.--,.,/,...-.,--+-,-..,,-.++,,/-..--,,./..,-.--,-,.,,/-,,./21./.-,-,+,.-,+,,,.-..-.-/-,.,-,-++++++..,,---.,-++-++-*-++*+*+*+*-+/+,+++,*))*+***,****+,-,-,++,,+**,+)*))++**-)),*+*,+-*,**),,*</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="101" 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">
101
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext">@25</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="102" 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">
102
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCGAACGACAGGAGTCGAAACTGCATTCAGTAATCCCTTCAGATGATCCGCAGGGGAGCGTTTACATATTGCGCAATGCGCAGGGCAATTCAGTCTGTAAGGGTAACAATGCGTTTACCGGCAGGCTGGGACATTGTGCTACGCGGATTACAGGCGTCCTTGCGAGCGAGTGGCTGGAAGGCTCCGACTTACTCTGACAAGGGACGAATTTACCCAGTTGCAGGAGCCACATGCTACAGCATTCTACCTTTGGTCGCCGCACAGCCGGCATCTGGATGGCAGAAAAACATTTGAGAAGTGACGACTACGCGCCTGGGACTGTGCGCACATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCGCGCGGTGGTCTCAGCGATTAGCCCCAAGCAGATACGC</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="103" 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">
103
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext">+</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="104" 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">
104
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext">/..-/0//001//.--..--,-.//.-.---1-...-/---/./-1.1./.--2--,..-,--+.+,-+,--...,--,.,-..-/..-.,-/.-0/0.-,-,/,-./--,-----.---11/..,./0////.-.0./.1-..-/----0/.0./.,,-,-,,-.-,-.../2,,.,,++,,.---.++**+0,,,,++****)))++*+***+*-+)+**,)**)))+***+,+*))(()**(*)(+)*)))*)+)*),+*(((*)(+*++(()())*+**)+**)))**++*+**++++-+,+,+**+*+)***)***++++,+,++++,+.,+*+,*****,,.,+,,,++)*)*)**+*+++**++,+0,,0+++-*+,,++,.+*,,,+,,,**+*,*)*)*,++++++,+-+,,,.-,--,+,.-.--..--,,---,,-0/--,//--.-..--..0.-...00/</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="105" 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">
105
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext">@26</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="106" 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">
106
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext">ATGGATCCATTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCTCATGACAAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATCAGCCGCAGGGAGCGTTTCACATATTGCGCAATGCGCAGGGGGCGATTCAGTCTGTGGCTGGCAACAATGCGTCTTACCGGCAGGCTGGGACATATTGTGTGTCAGAGCCGCAGTCCACAGGCGTCCTGCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACAGCACGAATTTTACCCAGTTGCAGGAGGCACAATCATCAGCATTTATCTATTTTGGTCGCCGCACAGCCAGGCATCTGGATGAAGCAGAAAAACCGATTTACGATCCCCTCCGCCTGAGCGGGTTGGCGCATTACGTTGTGAGTTAACCCAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGAGACTAGCGCAGGCAGATACGC</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="107" 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">
107
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="108" 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">
108
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext">-0-,--,--,-.,,,,,--/,,,.,,,,,-,.,,,-,.,,-/.--.-/./.-,--,-1/-./.,--..-.,-.-//.-/.--./.000//.1/.11/.00---.--/-//--.-..-..-02./-,0--.////..-/-///,//--+,-+++--.1,,.,,.,+-++,,+-++,-.0++-+-.***,,,,,-,++**,**,+-,++**-**-**,++,.+*+*+++-,0,+.++,-.+.--,,-,--,++*-,,--,/.--,-,,,-,-++,,-,,------.,*-*,-,+.+++,,,++-+.,,--,-,+,++++,-+*+++--,**+*****.+**+**++)-+,*-+****)+*)*))***,++-)))*))+*+**+++,,-,+*++++-,++-*+*.,3++,,.,,*.++-+-++++++..-..,--.,-,-.,--,./-.-.0....,..,/.--.--.---.-1/...-.-,-0-//-</span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="109" 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">
109
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext">@27</span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="110" 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">
110
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">ATGATGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATCAAAGGAGTTGATATGGCATTCAGTAATCCCTTCGGCTGATCACGCAGGGAGCGTTTTACGTTCTGTACACAATGCGCAGGGGCAATCGGTCTTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGGAGCCGCATTCGCAGGCGTCCTGCCAGCAGTGGCTGGAAGCCACAGGCGTACTCGACACCGACGAATTTACCCAGTTGCAGGAGGCAATGAGCCAGCATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCTAAGAAAAACTGTACGAATTTACCTCCGCCTGGAGCGTGGCGCATCATGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGC</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="111" 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">
111
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext">+</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="112" 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">
112
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext">..0..00-/1../--.--.,-/.--,/--./-/.//.-.//.0/0.//02/.-0.0/.-../----,,/.-.2..-...---./0-.0.-/-.../--/-,.,,-,,++.-,-,,.,,.1---,,-,-.--,,,.---,./---++,,--,,+,,,,,,-,,,-,,,,,,//.--2,.-,,,,,-+---.1+++*+..-,-,-+,,,,+,+,+,+.,..,,/,/,+++,,,,,,,--.,,++-+-.,+-,+,--,--,,+-,//-,-.,/..-,+-+--,-,-,,,,.+,-,,+0+**-,+--.,-,,,0,++++***+*))++)*)**,**,*,++++++*+*))*,,//,+,)),))))))))+**-*.++,+,,--,.+,,-,,-+,,,+,++--,-,,+++,,-+,,00/.0...-0./.00//..00./.,./-.-,--,-/-,-..---......0/2//</span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="113" 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">
113
</td>
<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext">@28</span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="114" 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">
114
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAAGGCTAATCGACCTCTGGCAACCACTTTTCCATGACAGGAGTTGAAATATGGCATTCAGTAATCCTTCGAGATGGTGCCGCAGGGAGCGTTTTTACATATGCGCAATGCGCAGGCAATTCATCTGTGGCCACCGCAACAATGCGTCTTACCGGCAATAGTAGATGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACGACTGAATTTGAACCAGTTGCAGGAGGCACAATGAGCCAGCATTTACCTTTGGTCGCCGCACAGCCGGCATCTGGATGGCAGAAAACTGTCAGAGATTAATAGCTCGCCGCCGGAGCGTGGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATCTTACTGGCCGCGCGGTGGGTTGTCTCAGGGACTAGCGCAATAAGGTTACGC</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="115" 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">
115
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext">+</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="116" 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">
116
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext">/..--.../00.--,,-...-../0..-,--.---,,,,--.---,--./,-/,-..-----+,+,.,-,---,,-++.,----,,0,-.---.,--,-,,,.,,.--+/.,+.-,,--+-...-+,,-,,.,,,,*,,,,++++,*++*++,-*+**-********+++,.+*,,++++,+***++,++,++,*+,,,,+*.*,,+-1+*++-,,,/-,0+++,+-+,-.+-,-----,---,-.....-..-//0-.--..--./0/./0,,//-/00----.-.-,--,--///--.-/-.-..,,....0,/-,--,...,/,,-.-,-,--,,---,,/,.......,,.+,,+,-+.++,+,.,,,,.+,+,,-.,,+-,-.,,.,,-,,-,+++**++*++,--,,+-+-++,,+*,,+*,*++++,-,,,+-,+**,++*+*,+,,,,,,,,,,,+++*++****-+-</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext">@29</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext">ATGATGCAGATTTGTTGGCGCGTGGCTTGATGCAGGGGCCGTAATGGCGGGACGGTTTCCATGACAGGGGAGTGAATATGGCATTCAGTAATCCCTTTCGATGACCATCCGCACCGGGAGCGTTTTACATATTGCGCAATGCTAAGTCGAGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCATAGCCGCAGTTACAGGCGTCCTTTCAGCAGTGGCGCTGGAAGCCACTGGCGTACTCTGACACCGACGAATTTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTACCTTTGGTCCTACGCACAGCCCGGCATCTGGTTGATGGGCAGAAAAACGGTACATAGAATTTACCCTCCCGCCTGGAGCGTGGGCGCGTACGTTGAGTTAACCGGAGAGGTTTTGATTTCGCCATTACTGGCCCGCGCGGTATTGCCGGACTAGCGCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="119" 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">
119
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</td>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="120" 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">
120
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</td>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext">++-++,,,-)/.++,+*+++++-+-,++,+-,,+-,*+-*.+,/--0+.+,+-,--,,+,,+.,,+,,,,--,/--...-/..-..,,/-.-.0..,.+-+-,--+.,,.,--.,,./..23---,---..0-.,,,,.,,,+,+++,**,-*++++,,+,++,+,,,.++***-,+-/,,,**+**+*+**+-*+**++,-,-.,,,,,,+,/,.+,-,++,--.,4+-,++,,++,-,-----.---,..-.-/-.-/..----/..--//--//0---,./.,.-00//0./-../-1.-./101.--/.----/.-.-0---+-,-+,00-,./././-0/-.-..-.-,/.---,,,,...0/-,,+--,,,/1/....-...-0..,//---.2/-,.1-0..,-/--------,,/2-..,/,/--,1-.-.,,-.-/-.-..,-,,-,,,++++,++-,++-,,,-,1++-,++-+,,--,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="121" 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">
121
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</td>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext">@30</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="122" 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">
122
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext">ATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACAAGGATTGAATATGCATTCAGTAATCCCTTCCATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGAAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGGGCAGGCTGGGACATGTGTGTCAGCCGCATTGGCAGGCGTCCTTCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACGACGAATTTTACCCAGTCAGTTGCAGGAGGCACACAATGAGCCAGCATTTTACCTTTGGTGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGAGCCTTGGCGCATTACGTTGAGTTAACCGGAGAGTAGGTTGATTCACCCATTATGGCCCGCGCGTGTGTCGTTTCGCCGGACTAGCGCAAGCGAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="123" 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">
123
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</td>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="124" 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">
124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext">,,,+,,-,.,,-,,-,1---..-+-,-./1...-,,--,.-./----.--../..0////./.10-/--.-//,-/....-.-,,-.,/1.1/.-..2//10.///-...1/.-,,.../.21.00-./----...-.0//13/---..-,--,-...//-0-,,0.-/.---,,/--.,---,-,----2.--,.----.0.-//--,-,,-,,.--,--,--..0,/,.-...-..0//000---..0.,0-.-.-,.-----/0/-///0//-//0/001/0-../..,/,.-.+..----/-.-1.0....//2../-.0.020---/,,-----.,-----/,-----.-,.,,,-.----0.--.0,,,-,,,/,,+--++,---/,,,,,+--./-+/,,-,...-./---/-,0.,+.,,,,--,,+,.,.,,-.-,,----.-/,.</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="125" 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">
125
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</td>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="plaintext">@31</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="126" 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">
126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext">AGCCAGCATTTACCTTTGGTATGCTTCTCGGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAAGAATTACCCTCCGCCTGGAAGATGTGGGATTACCAGTTGAGTTAACCGGAGAGGTTGATTCGCCCGGTCAGCCTGGCGGGGGGTTAGTTGCCGGACTAGCGCAGGCATCAGGCTG</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="127" 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">
127
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext">,,,+++-./-.,-,..,,,,+.,--*-,+++,+,,+++,++.,,,,++++**++**++-,*,+++))*+)**,*+*++.+-+,.++-.-+--++++++***++,*-+*,)**+)))+,*,+.,.--,,++*++****,+*,**,*)*++*,-**+*++*+*,+**+,+,,++,**))))(*,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="129" 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">
129
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</td>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext">@32</span>
</pre>
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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>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext">GTGATGCGCTTTGTTGAGCGGTGGCTTGATGCACCAGGGGCTAATCGAGACCTCTGGCACCACTTTCCAGTGACAGGAGTGAATATGGCATTTCAGATCATCCCCTTCATGATCCCAAGGGAGCGTTTTACATATTGCGCAATGCCAGGGGCAATTCAGTCTGTGGCCGCAACATGCGTCTTACCGGCAGGCTGGGACATTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAAGTGCTGGAAGCCACTGGCGTACTCTGACACTAGACGAATTTGGGCGTTTGCAGGAGGCACAATGAGCCAGCATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATCTAGCTCCGCCGGGGAGCGTGTGGCAGTATTACGGTCCAATCGGAGAGGTTGATTCTACGTCTATCGGCCCGCGCGGTGGTTGCCGGACTAGCAAGCGAATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="131" 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">
131
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="132" 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">
132
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext">)+**++,++*++,*++*,+,*+++**)+**+,+)))-*++*)*++*,*,+++,,-+,**+,,-,-,+***+++,,,,.++.+,,+,++,,+++,+,+-+,++++,+++*+--,,,+,+++---00-.,++,--+,,,,+,,-,.-,,.+,,,.--,-.,...---.-,,,,//.-./,++++,,----,,/-,,,,,.,.-.-,,,,,,,-..,,,,,,-,/+******+++++,++++,+***,-,,-,,,+-+,,+,0,,+,,+,++,+,++,-+,+-,,,,-+,---+,/+,/0,1,,,----.-,-+++,-++*+**+,+++,,++*+++,+,+,+++*,+,+*+.+/,**))(()*()()()()()**)*))*))*+)))+))*))**))+(()(((((((()*(*)))+*)**)****))**)********+*))*))))*))*+***+++++*,**,*+++</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="133" 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">
133
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext">@33</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="134" 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">
134
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGCTAATCGACCTCTGAACATTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCTTACCGGCAGGCTGAGACATTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGACGTGGCGCATTACGTTGAGTTAAAGCCCAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAATAGCAGATACGC</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="135" 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">
135
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="136" 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">
136
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext">+,-,,,,--,.,,-,,,--/-,-.--.-/-//0--,..,..--///.0..--,0-.,--,,,,+,-.,,,-.+,,,.-/--,,,,-,-,,,,..-.,/-,,,,--.--,---/--,-,,++.-.-.-/+,,-.-/2+--.-.---.-.---/-..--..--,--.-/-..----..-.....-.---...//---/,/--..-,,-,.-,+--,,,-//-,--.....-.--..,./..-..../--.----,-..-,---/---,,.,..-..-,---/--.,,-/.0---//--,-.----..---.-...---./////..1//./0../-.//./3/32./-....02/...////100/0/00222/102210/0110/0////./.,../1/0/.../...12/010/3/122/..////.-.,..,-----./-..//../.-0..//0/100</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext">@34</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="138" 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">
138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGGGCTTGATGCAGGGTAATCGACCTCTGGCAACCACTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCGCAGGGAGCGTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGCGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAAGTTTTTGATGAGTTGCAGGAGGGCACAATGAGAGCCAGCATTTACCTTTTGGTCCCGCACAGCCCGGCAGCCGGATACAGAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGGGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACCCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="139" 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">
139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext">-.--.....--,,++++/,,,,.--,-++-,,++,,,,,-,/-/-/.---/,,-.----*++,+,,,.--+,.-,,-,,---.--,-.01-./00-/-,-.,--.-.--,-,-.1..--..300/.--.0./.....0//--./0./,,..---,,-,,,0,,.---0,.-,-,++,,,/-,---,,+--,,,,+++.***+**+.-+++,+.++,--++*+-,,++*-,+,1,+,,+**++*+++,-++,++.+++-+--,,,,,,-,,,,,+**,+,+,/+,,,+,**,+++,-+++,***+***-*+,))*+*+*)*)))*),+++,+,+++,*)****))))(+(**+))))(()*-*+*)*+****+***+**+-****)***++)+*****++,,++,,+,,..-,,+++++,+*++++-,,,-++,+,,,+,-+,+,,,,,.,,-,,,,.,,,++,+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="141" 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">
141
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</td>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext">@35</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="142" 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">
142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext">GAGTCGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACTCACTGGCAACCACTTTTCATGACAGGAGTTGAATATGGCAATTCAGTAATCCCTTCGATGATCCGCAGGAGCGTTTTAAGTTTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGCTGTACCGGCAGGCTGGGTTGTACACGCGGATGTTGCATACAGGCGTCCTGCCAGCAGTGCTGGAAGCCCACTGGCGATACTGACACCGACGAATTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTACCTTTGGTCCTGGGACAGCCCGGCATCTCAGGATGGCAGAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGAATCATGAGTTAACCGGAGAGGTTGATTTCACCTTATACTGGCCCGCGCGTGGTTGCCGGACTAGCGCATAGCAATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="144" 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">
144
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</td>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext">--.,,/-.---...0--.-----./.-./-0..--.-/.-//./--0/-../..--0.000../..--../././.--......./.....-.--/../0./...-.-..--10.-.-..../.-,..0.--./....0/....-00..0////..0.//./.--,-..//./.,/---/...-/..//.---0.1-,00.//-----,.-..-,-./-0-,+-,..-.../--/.,,-/-./-..-.../----/-../-.--,-,..,,,,.,.--/-.-,-/+,----...,.,-,/-,,+,,,--,,+,+,+,++,-,----/---.--,-,,.------,-.-.-,,-+,-.---.,0-,,---...-.-/01--/..+..-/--.-/..-.,.,.0/----.-,-.---.-//..-.....-----,//--,---,/.---,.-0./--..-</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="145" 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">
145
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</td>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext">@36</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="146" 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">
146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext">TCACTCCCGGCCGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACAGGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCATAGGCTGGGACATTGTGTCAGCCGCAGTCACAGGCGTTATGCCAGCAGTGGCTGGAAGCCGACGGCGTACTCTGACACCGACGAATTTACCCAGTTGCAGGAGGCACAATGAGCAGCATTTACCTTTGGTCCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCTCCGCCTGGAGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" 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">
147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="148" 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">
148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext">++*)))**+++**+++-,+,+-,,*+++*,++*+,+*+++--,-,/,,++++.+-.----.-,.-100..---,-....-../-0.-.////////0./-/11001/0000/0/1610/..11211/10./100221010/01//1/021002/0/../...--/0.0/1-00-/.--.,.-.-/--,-,,-,-...--,,+,,,,.-,,-+.,---.-.-,---,//.-/0/-.--.-/00./0.//.-..1.3.//0/..10131131..-01100/---/1.-../12///.0..//..0.//20...----0--..--,-,..-.,./.-.-.-/,,/..0.-,,,,/-/..--,,,-././......--...//.-.----/-,-.-.-.-,0--./-/-,-/--////..-----,-+-.-.,-..,,//./..0.././-..0/.</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="149" 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">
149
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC149" class="line" lang="plaintext">@37</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="150" 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">
150
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</td>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGCTAATCGACCTCTGGCAACCTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGGGACTTCGCGCAGGGGCAATTTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATCAACGAGTTGCAGGAGGCAATGAGCCAGCATTTAGTTCTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAACTGTCAGAATTACCTCCGCCTGGAGCGTGGGCATTACGTTGAGTTAACCGGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCACATAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="151" 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">
151
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC151" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="152" 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">
152
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext">,,.,,,,,+,-,,,-+,-,,.,,-,,,,.+,./---.,+,..///./2..--,+,,.-.--./.-./1.0-..-..-./-.-.,,.-,,-.-..--,-,,---,-1/./..0.-/1///--/1//100.-.-.-..0/.2.///..0/0/00/../1//..//0.//0/02/2102..././3/00/00///..000000/...//2/01../.0././---.-/-,---.--..,,,+-,,.,+-,,,--0-/,,.,,,+,,**)+)*))+*)**++*,+*****+)*-*+,***+++-.-++)*+*++*)*****,+++,----,,--,,,./-/.,-++,+,/1//.--,,,/---,.--.//./00./////../././0./.---//...00.--,.-/---0.-../..-/-.../0//..,..-.-/.-,,/.---./..-,---.,,-.0.</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="153" 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">
153
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext">@38</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="154" 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">
154
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGTGGGCTTGATATGCAGGGGTAATCGACCTCTGGCAACCACTTTCCATAGTGACAGGAGTTGAATATGAGAATTCAAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTACATATTGCGCTGAATGCCCGGGAATTGGGATAGCCTAAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCAAGCCGGGATTACATCGTCCTGCACAGCAGGTGCTGGAAAGCCCACTGGCGTACTCTGCTAACCATGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGAGCCAGCATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAAGCGTCTCCGCCTGGAGACGCTTAAGGGTCCATTTGAGTTAACCGGAGAGGTTTGATTCGCCATTACTGGCCCGCGCGTGGTTGCCGGACTAGGCGCAAGCATACC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="155" 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">
155
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="156" 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">
156
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC156" class="line" lang="plaintext">-./-.....-./,--,,-/,-,,,-,-,-+,..-,,-,,+.,.,,-,---.,,,.-./-,-++++,+-.,,.,,-,-.++,--,--,-,,/,,+,--,,,,--,,/,,-,++*--,,--,+,.,,,,*++,,,,-,++.,,,/-,,,,-,-,.,-+++-++++++---,.+-++*+*+,,./-/-,,+++-,,-+,,+,++*,-+*++-,+*+*+++,*+*++*,,,),+**,,**-**+**-**+*,*+,+++**-+*,)),*++-******++*****+-,,,*)****),,-+*,+/****,++++,*++,+,++++++++,+,+++,+,,,++--,+,-,,,-,++**,.--,,.+++**+++*++,++,,+,.,+,+..,++,+++-+-+--*+.++++*+++***+*,,++*-++,,*++,+++*++++**+++,,,,+,*+,,+*,,++,,,-,,,,-,-++,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="plaintext">@39</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGGTGGATGCAGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGCGGAGCGTTTTACATTGCACAATGCGCACAGGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACAGTGCGCAGGCTGGACATTGTGTGTCAGCCGCATCACAGGCGTGCTCTGCCAGCAGTGGCTGGAAAGCCCACTGGCGTACTCTGACACCGACGAATTTACCCAGTTTGCACAGGAGGCACAATGAGCCAGCATTTACCTTTGGTCGCCGCAGCAAAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTGCCTTCAGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTTGCCATTACTGGCCCGCGTGGTTGCCGGACTAGCGCAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="159" 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">
159
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</td>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="plaintext">----...----.,.,,+,++-*+++++/-,--..,--.....-/.0/-,+.,-/-..--.,,,,,-,,-......./....0--0/--../--.-,,,--.//...-.-.-/--./.-.--,//0..,,,,0/---,,/----,---.-/.-..0.,.,--,/,+,-......-,,,,,----,/-./-.,/,,.////.-,,,,-,,,-.--,-/.-,1,-+,++,,,-,-/1--0/,,-++,,,0++,+.+,,,,++,-,,,.--,+,,,-,,,-++,-.,.,+-**-++--+++++-,.0-,,,.,-.../-/.0.---,,,----,/,,/,,----.1/.-.0/./../.--0/130201.-.../----....--....0../0///023/...1..0001//0//.3./..-/,--//.0./11.-./////.//4/..../.../..-,.--,--/++</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="161" 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">
161
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC161" class="line" lang="plaintext">@40</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>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCGTGCTTGTGTACGCAGGGGAGCGTTTTACATATTGCCAATGCGCACTAGGGGCAATTCGGTCTTGTGGCCGCAACAATGCGTCTTACCGCGCAGGCTGGGACATTGTGTCAGCCTCAAGAGCAGCCGGAGTCGGCCAGCAGTGGCTGGAAGCCCACTGGCGTATACTCTGACACCGACGAATTTTACCCAGTTGCAGGAAGAAATGAGCCAGCATTTACCTTTAGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGCAAAGCTAGCGCAAGCATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext">./01-10//0///1..///1/.//0//.2//001.//10.1100000003/33/.2/12101/.///.0/0//0500///00/1///0.12//0///00/000,/-/-/-----.---/-./0/--,,.-/.1..-,././.-,,.,-,-,.,---,,-,//+-,,+,,++,+++./-...--+-+,+++*+,,--,,++,/-.--,,+++--,++-,.,----///.,..,,.,+-,---./-.-,,,+-..,-,---,.,,./0..-.1//1.--.-/.//.-,/,--/.--/-.,-,,/,../---.--.//./-..1-,+.,,,-/--,----,-,-/-.-..--.-0-----012//./-,/,.-,,.,/.-/./-..--../1--/0-/0.-./1/0....-0//.--.--.,/-0.-.1.-.../1-//-.--...-.,-0/.-0.,0-,/...--013,-.-.--.3//</span>
</pre>
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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>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext">@41</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext">ATGAATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGTCCCAACCACTTTCCGCTGACAGGAGTTGTAGAGTATATGGCATTCAGTAATCCCTTCCATAAGGTGATCCCGCAGGGAGCGTTTTTAGATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCATAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACATACCAGGCGTCCTGCCAGACAGCAGTAGCTGGAAGCCCACTGGCGCGGAGTCACTCTGACACCGAGCAGGACGAATATTTTACCCAGTTGCAGGAGGCACAATGAGCCGGCATTTACTTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAACTGTCAGAATTACCCTCCGCACTCGAGCGTGGGCGCATGTCAATCGTTGAGTTAACCGGAGAGGTTGATTCGGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="168" 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">
168
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</td>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext">.-/-,-...../---,,.,-.,.-/-,,,,--0/+.--.,,..//.1,0-0//,,,--..1/.--,,-/,,-,,.--++.,,,-.-,,.-*,,,2+,.-++,*,-,,,-,-*-*+-+,,++.,+-----.--06/--,,+,,,,-.,,-+0,../,-,.**,++,-,./-2.,-0,,,0--/+.,--.--/..-0-.-,,-.---/,/,,.---./-/,+.,+.,,,-0--,/1*/-,*,,,.,*+*++,++,+,++,-+++*+,+*++++*++++.-,++**))**-***,)+*,**,,+****)+*-).+*+-+*++++++.++0*++++++,---.-+,,.+,.,,/*+,/--,,,,,--,-,,.+.-,+-,,,,/--++,-,+++-+,,,,,+*++-,-,++-,,,,--,++,++,-,,.*,,-,,-+,.-++++,,,++-,*+*+,+,+,,+++*+,+,-**,,,+-.,+,.+,-,-,++-,+-,,+++,,++++,,.,---.,-,,-,,</span>
</pre>
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<td class="diff-line-num old old_line" 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">
169
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC169" class="line" lang="plaintext">@42</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="170" 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">
170
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCATGACAAGGGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGAGCGTTTTACATATTGCGCGCACTTCGCGCAGGGGGCATTCAGTCTTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTACCCAGTTGCAGGAGGCAATGAACCGAGCATTTACCTTTAGTCGCCGAAGACTCATGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCTCCGCCTGGTGGGAGTGGCGCATTACGTGTTGAGTTGACAGCCGGAGAGTATTGATTCGCCATTAGTTACTGGCCCGCGCGGTGGTTCCGGACTAGCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="171" 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">
171
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="172" 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">
172
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC172" class="line" lang="plaintext">..0.-./0-../..---..0.-....--0./00---./.-/0/0100/3//1..-0.02000/./..1/1./1///000/00/0/2/0111120/0/0/00..0././0//.1...//2..2...-,.0/.2.0---.-/-,--.-/..-,.,----....,-,..----,,-+,,//./0,-,+--,,-,/.-.0,0,,-112/1/./.-../02/10./0./201/2..////////10/202.//..00/00.-0-0.0./..3./01-1.-..-./--.,-,-.-//--+,+-+++++,1.*,+-+,-0/--+,,0+++**+++*-+++++++++**++++-,-..,,,,++,-..,+--+,+,.--,+++,+,-++++.+-.+,/,0,,./.--.+.,+,,,,.,0,,--,/.,,-,+,+,+.,-,.,,-..-,,,+,,---.++,,/,,+,/,,,.,,,-.,++,-+,.-.-.,--+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="173" 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">
173
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC173" class="line" lang="plaintext">@43</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="174" 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">
174
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC174" class="line" lang="plaintext">ATGATGCGGGTTTGTTGGCGCGGGCTTGATGCAGGGGGCTAACCCACTCTGGCAACCACTGTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTAGTGCGCAATGCGCAAGAAATTCAGTCTGTAAGGGACCAATGCGTCTTACCGGCGGACAGGCCCTCTTGTCAGCCGCAGTCACAGGCGTCCTGCCGGAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAAGGAGGCACAATGAGCCCTCAGCACCATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGCTTGGCAGAAAAACTGTCGAATATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGGCAGTGCTGGAGAGGTTGATTCGAGGTTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCATACGC</span>
</pre>
</td>
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<td class="diff-line-num old old_line" data-linenumber="175" 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">
175
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC175" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="plaintext">,,+++,,,,,-.,,,++.,---,-,.--.,--,,.--,,,,.,,....//../-..1...,/--,.0/-0///..--/,,-/.-./0.--.2,.0../0/--/,,-,,,-,+,-------/-++***+,+*+.+,-,*+*****,**),)(*()()())*)*)+)*+,***)())(+*++*)****+)+)***),)))*)+*,*+*.**++0+,,**.,****++-,+.-+++,++,,+++-,-.----,--,-,-.,,,,-,/--//-+-+-.--.+,+/.,.,-/--/0//0-..,.,-.-0--./.0,-.00/.,,,,--,/--/..1...20../0/-10---,0-////1--.-,--//-./-.....-0../..-./.-,--.0-,--0.,+,,,,,-,+-+,+,//--/,--,+-,,,--+,-++.+,,,-/,,-,,-,,++,,-,,,,---,---,,,.0,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="177" 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">
177
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC177" class="line" lang="plaintext">@44</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="178" 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">
178
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC178" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCAATCGACCTGGCAACCACTTTTCCATGACATAGGGTCGAATATGGCATTCAGTAATCCCTTCAGTCGATCCGCAGGGAGCGTTTACATATTGCGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACTACCGGCAGGCTGAGAAGATTGTGTCAGCCGCAGTCACAGGCGTCCTTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTACCCAGTTTCAGGAGGCAATGATAGGGATCTACCTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAACTGTCAGAATTATGCGCCTGGCAGTGGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCAGGGTACTGGCCCGCGCGGTGGTTGCCGGACTAGCAGCAAGCATACGC</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="179" 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">
179
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC179" class="line" lang="plaintext">+</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="180" 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">
180
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="plaintext">//1/.1/.///0/100/001/.//0...1/./0./-.0//2//001.2/.--0-//../---.--,,-.,,--,,+.--/.--...-./-,-..----,,,,,-,,,,,+/,.--.-,-/,.,+.-/../.,-+.+,,,+,-,,++++*+-+,,/,-,,,-,,,++++.+---/0---*++-*+++++,-,--+,+++,,.--.-,,,+--,,,,,,,-0--,1,,,,,,+,--+..--.0-/,,.,-/--0----./,.-,,/,,--,-,--/002/-,,,.,.----/-.-,,--.-.--+-.,-../--.1..----../.-.-/.0....00/0/././..//..211/0///0/110/./0..1/0////0/2../.00/..00//../..../-.-...0/0.2/..../.-.-,,--.0-.--.---.,-/--,//-,-/--,--,.,,,-.,+,,.+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="181" 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">
181
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext">@45</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="182" 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">
182
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext">ATGATGCGGCTTTGTTGGCGCGGTGAGGTTATTAGCAGGGGCTAATCGACCTTAGCAACCACTTTCTAAGTGACAAGGAGTTGAATATGGCATTCAGTAATCCCTTCGGATGATCGCAGGGAGCGTTTTACATACTGGTCGCAATATTGCGCGGAAGTGATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATGTGTGTCAGCCGCAGTCGCGCAGGCGTCCGTGCCAGCAGTGGCTGGAAGCCACTGGCGTACTCTGACACCGACGAGAATTTTGACCCAGTGCAAGGGAGGCACAATGAGCCAGCATTTACCTTTGGTCGCCGCACAGCCCGCAGGCATCTGGATGGGCAGAAAAACTGTCGAAGATTACCCTTCCGCCCGCTGAGGGTGCGCATTACGTTGAGTTAACCCGGAGAGGTTGATTCGCCATTACTGGCCCGCGGTGGTTATGCCGGACTAGCGCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="183" 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">
183
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="184" 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">
184
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</td>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="plaintext">,,,***),..*,**)))**)+***+(*)*)))*())+***+*)*+,,++*,****+*,+-,+*,)))+**-*+**,+,++,**+,---,,-,+-,,+.-+,++++-*,***)))*++,+,++,--*+***+-*-+/+,*)*,*+**,*+))*)**())()*****,**,*)**)))*+/-+./,,+*)*))+*,,,+-*)++*.*++++++++.++++,-++,+,,,,,-/-+*,*,**+-,0-,+,+,,++*++,++-+,-,,,-,-,-+,-,.+-,--.,,.+./,+,.,-,,,.+,+--.--+,,+-.-,-++-,--2.-/++,,,.++-,*,,+.,-,-,,,--+++,,++,+,*++,*++++.,,--,+,-**,,*+,,+-,--++,,-*,++++++++,,*,,,+.,-0+++,+.+++*+**+,,.,-,*-**+*++*+*,,*+-,+*++,+*,+*-****-******)+,*+**+,)*+)****</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="185" 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">
185
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC185" class="line" lang="plaintext">@46</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="186" 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">
186
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC186" class="line" lang="plaintext">ATGATGCGCTTTGTTGTGGCGCGGTGGCTTGATGCAGGGGGCTAATCGACCTCTGGCGGACAGATTTTCCATGACAGGAGTCGAATATGGCATTCAGTAATCCCTTCGATGATCCTAAGGGGAGCGTTTTACATATTGCGCATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTATTCCAACACCCACAGGCGTCCTTGCCAGCAGTGGCTGGAAGCCCACATGGCGTACTCTGACACCGGATGACGAATTTTACCCAGTTGCAGGAGGCGCACACGCCAGCATTTACCTTTGGTCGCCGGCACAGCCCGGCATCTGGATGGCAGAGACGGTACAGAATCCCTCCGCCGGGTGAGCGTGGGCGCATACGTTGAGTTAACCGGAGAGGTTGATTCGCCATCTTACTGGCCCCACGCGCGGTGGTTGCCGGACTAGCGCAAGCATCAC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="187" 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">
187
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC187" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="188" 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">
188
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="plaintext">-.0--.//,.-.--.-.,.,-.-,---,,,-++02-,,,..,+,.,,-,.,.,,/.,,*,.+,,.,,*,+,,+*+,,+-++*-,+,0+--,,+.,++.,,,,,-+-,,+-.-,,,++,,,,--,17/.-,-0.3/0.0-,/.-..,.--,./-..---,../,,,.--,,,,./01,0.,-,+,,+,-+,/,,-,,,,,.//-,,,+-,,,,+-/-+++,/-.,.,++-,+-*+/,-.++/,++-+,+-0-++-+++-,-+,,,-.++,,-,,-+,,.-,,*,+.,**,+,+-,,+++,+++++)++,*,++**++,,,+++/-+++,***,****,,,,-,,+-,-+-,.,---.0-.,+,,,,,//,-/-,/-,,--.--,,/./.01/..-.001./021..--0...-1../..0//.0.1.2/-/-..--.....//-011/0.--,/----....-0...000-.-/.,,,-.</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="189" 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">
189
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC189" class="line" lang="plaintext">@47</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="190" 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">
190
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC190" class="line" lang="plaintext">ATGATGCGCTTTGTTGTGGGGTGGATGCAGGGCTAATCGACCTCTGGCAACCACTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATTGCAGGGAGCGTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCCTTGGCCGCAACACCGTGGCGTCTTGTAAGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCCACAAGGCGTCCTGCAGCAGTGGCTGGGGAAGCCCACTGGCGTACTCTGACACCGGCCCGAAATTTTACCCAGTTGCAGGGCACAATCGGAGCATTTACCTTTGGTCGCCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCACGATTACCCTCCGCTGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTTATTCACCGCTTACTGGCCCGCGCGGTGGTTGCATTAGGACCAGCGCAAGGGCAGATACGC</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="191" 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">
191
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC191" class="line" lang="plaintext">+</span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
192
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC192" class="line" lang="plaintext">/---./../--+*,+-++,-,-,+,+0,,.,,.,.../,-,--,-,,,,,-.-,,,+*+++,,-,-,,..,,---.-.0/-....0-./--/-.,,.//----,----.-/./-/--/1/0/0.-1///0-.----.-.,/.01.,/.,,-/-,-.-./0--../,../.-0,,,.,.....---,,1,,--,,/,++++,,,.,-,,*++,,,.2,+,*++,,,,.,-..----++-++-,+,/+.++,++--+-*+,/-,,,,-++,,-..-,+-+--.,,,+,,-,,,,-,++,+*+,---.+,-/-.++++*+++*,/,+,,-+,,+/+,,+++**,,,++-,,,.,.,++*,,++,*+++**+++,,++,,+,+*+.,+,.,/,+-,,,+++*+**++++++**)-,++*,,++,.+-+,.+,--..---/+-+.++.+++,,-,,,-,..-,-./.-.,....</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="193" 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">
193
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC193" class="line" lang="plaintext">@48</span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="194" 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">
194
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC194" class="line" lang="plaintext">ATGATGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGAACCACTTTTCCCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCCGCGCAGCGTCAGTTTACTCACATATTGCGCAATGCGCAGGGCAATTCGGTCAGTAGCCGCAACAATGCGTCTTACCGGCAGCTCGTGTGTCATAACCACCCGGGTATCTTCACGCTAAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCGGATTTACCTTGGTCGCCGGCACAGCCCGGCATCTGGATGGCAGAAAAACTTCTCAGAATTACCCTCCGCCTGGAGCGTGGCATTACCGTTGAGTTGACCGGAGAGTGTATCATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACGACTAGCGCAAGCAGATACC</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="195" 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">
195
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC195" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="196" 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">
196
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC196" class="line" lang="plaintext">/.20///../0..-..-/.,..--.-1---.--,-..-/////...-,--,,--------+++-,,+.,+,---,-,,+-,,,.-,,,,,--+++++,,,.,+,,,,,+-.*.++-.-,*++-+***,*-,-++.+,*)*-++-,+,,,+--,-,,.++++,+)**+***)**.,,-1*,*)*****)+,++*,*,-*-,,**)+++-+*+++*,+-,.,+,,,-,+++,0+-,+,,,,,+--,---,,++---0/-.-.-./0,-/.1----/..-.0-...-/0---1//./..--.2-0...-//0.,-0..0.,.--0-.-.-/,,,--.---,/0-..-,/..-.-/.-/---,/,-.320--.,,-,---+,-++.,.,/,.---../-,/-..--,/2,,,-.,,/-,,-,-++-+-+,*,,+-.-,-.-,.,-0/,-,-.-,,+,/++,+*,+++***,,**-/**+++*+**+**</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="197" 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">
197
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext">@49</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="198" 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">
198
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext">ATGAACGCTTTGTTGGGGCGCTTAGATGCAGGGGCTAATCGACCTCTGGCAACCAGATTTTCCGATGACAGGAGTTAGAATATGGCATTCAGTAATCCCTTCGAGTATCTGATCGCAGGGAGCGTTTTACAACTTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTGTACCGGCAGGCTGGGACATCTTGTGTGTCAGCCGCAGTTACACATGCGTCCTTGCGCCAGCAGTGGCTGGAAGCCCACTGGGCGTACTCTGACACGAAGCGAATTTTACCCAGTTGCAGGAGGATGGCACAATCAGCCAGCATTTACCTTTGGTCGCCGCACATCACCGGCATCTGGATGGCAGAAAAAACTGTCAGAGAATTACCTAGCCGCCACTGGAGCGTGGGCGCATTACGTTGAGTTAACCCGGAGAGGTTGATTCGCCAGTCACTGGCCCGCGCGGTGGTTGCCGGACTACGCGCAAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="199" 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">
199
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC199" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="200" 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">
200
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC200" class="line" lang="plaintext">-+,,,,-,,-+*+**,*+-***)*+)),))*+**))+*,,+.+,+,-+*+**+-)*****)**,**++**++++-+*.+++,,+--,++,++.*++,++++)*,*++,,,,+++,,.---,/5.-,-,--.-,--,+,/,./0,---++---,..0,-10-,/-,-.--.,.0/-.9--/,,.,,,--.0../---+,0-./,,-/-.,/+,,,-,.0+.-,+.-,.,.-,.,+,-..0-,-./,,/.--.--/,-,,,,--,-/,-/,/--,--,.//---,,./30.,,,...-0,-,,-,-++,/,-,..-/.,/,--/-00-/,-,.--,,.-,.,+----.+/.+-,-,--/.--.0...--/./000///,,/,-00/0/--/,-....0..../...00.0--..6.-..0..-.0..-,--,,/.,-./---/-.---/--.-/,-..--+,-,--++,,*-+,+++++,*-,,+,.,,-.3++,-,.,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="201" 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">
201
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC201" class="line" lang="plaintext">@50</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="202" 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">
202
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC202" class="line" lang="plaintext">ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTGAAACCACTTTCTCATTATAAAGAGTTGAATATGGCATTCAGTAATCCTTCTAGATGATCGCAGGGAGCGTTGCCCACTTAGTGCACCGCGCAGCGCAGTTCAGTCCTTACTAAACAATGCTGTTATAGGGCATCACCGGCTGGACATTGTGTGTCAGCCGCAGTCAAGGCGCGTGCCACCATGTAGCTGGAAGCCCACTGGCGGAGTTCTGACAGGACGAATATTTACCCCAGTTGCAGCAGGGGATACCGCCGCCCGGTTTGATTTATTTGTAGCCGCACAGCCCGGCATCTGATGGAAAAACTGTCTCAGTGTAGAAACTAAGGGCAGCCTGCCTGGGTTACTTCGCGTGCTCCCAAGGCGAGGTTTAACCGGTGATGAGGATTGGTTGCCCGACAACGCGCAGCAGATACGC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="203" 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">
203
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC203" class="line" lang="plaintext">+</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="204" 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">
204
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC204" class="line" lang="plaintext">...---2.-..,-,,,.,,,,-,,,,,,.,..,,,-,.,,-/-/--,---,-,,...--,,,,,+,+,,,--,,-,,-,,,++-0,++,,+--+,,,,,+,+++,,,+*,++**++,.,+*+**+++**)*+*.*)***,***,++**))+*)*,))+)*))**++,,+,*++*+*+**-,,+.,+-+,,+++-,,,,,,,,++*+,,+-/-,.,..-,,-.,,,,,,,,,,-,,,--+,,,/.,,,++++++-,-,+++++++*++**++.,++)))))*,++)*+++++*++*)*))****+**++*++*+,++**+++*)))*)****+*+***++*))))))))**,,+,,,)**++*+*))*+***)*)))++**,))*,),)))**)**)+*****),)))****))*+**)),*)***+**++***+*+***+****+*+++++*,,*++,++++,-,</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="205" 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">
205
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC205" class="line" lang="plaintext">@51</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="206" 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">
206
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC206" class="line" lang="plaintext">ATCATGCGGTTGTTGTAGGGTGCAATTAATGCCCGCTAATCGACCTCTGAATACCACTTCTAGTTAACATAGGAGTCAGTAATGTGCATGCAGTAATGCGTCGCTAATGATTAGAGGAGCGTTTTTACATATTGCATGCGCCACAGGGGGATTCAGTCTTGTGGCAAACACCTGCGTTGCCCGGCGATCGGCTCGAACTTGTGTAGTTTGTCTCACCGTACAGGCGGTTTCCCTGCCAGCAGTGGCTGGAAGGCTAATGGCGTACTCTGACTAGACAGCGATTTTACCCCATTGCCAGGAGCAAATGAGCAGGATTACCTTTATTGCCGGAACTAAGCCCGGGAGTACATGAATAAGAAAAACTGTCAGAAGTGGGTAGCGCCTGGGGTACTTGGGCGTGGCTCATTCAGTCTATCACGCGGGTCATTACGCCCGTACTCATGGCGCGTGAGTTGCACTAGCAGAGCAGCGTAGA</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="207" 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">
207
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext">+</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="208" 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">
208
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC208" class="line" lang="plaintext">-,-.,/--.-.-,,++,+++.,+-,-+,+.,-+,+-,+,,,,,,-,--/--,-.,+..,+,*+,++,--,,,,,--,,,+,-,,,+.-,/-,-.----.-.,,,+-----,,,.,,..,---.-,,+,----...-.0.-.+/.,,,-,,,,,.,-,,+-+++++*+,-,++-+,,+-+,,++./+-+)*++*+++,+,+-,+-**-*+++*++.,,.-,-,,+--++.,,-+,,,,,,-/,.,.--.,-.,-.+.-.-/.0-//--0.0--.-.0..00,/010,-/0/-----.+-/----,./-.--,-,.-.-.,.,.,.,/-,,++--+,,,,-,,+-**-,..,-++-+**-,,+--+*,,*-*,++**,*+*+,,+-+,++-++++-,.,.+-++,-+,+.+++-*+++,+.--++,-,-,,.--,,.,.,+--,,,.,-,.,,--+,--,+,,-/-.,../-/.,/-</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="209" 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">
209
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC209" class="line" lang="plaintext">@52</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="210" 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">
210
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext">ATGTAATGCGCTTTGTTGGCGCGGTGGGATCTGCAGGGCTAATGGTACACCTCTGGCAACCACTTTCCATGACAGGAGTTGAATATGGCATTCGCTAGTAATCCCTTCGATGATCCGCAAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGGCGTACTCTGACACCGACACGAATTTTACCCAGTGCAGGAGGCACAATGAGCCAGCATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCTAGAATTACCCTCCGCCTGAGCGTGGCGCATTACGTTGAGCGAGTTAACCGGAGAGGTTGATTCGCCATATTACTGAGGGATGGTTAGCAAGCGACCCTGCGGAGTTGCCGTTTTACACGCGCAACCAAGGATTTCGG</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="211" 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">
211
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC211" class="line" lang="plaintext">+</span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="212" 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">
212
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC212" class="line" lang="plaintext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span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="213" 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">
213
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC213" class="line" lang="plaintext">@53</span>
</pre>
</td>
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<td class="diff-line-num old old_line" data-linenumber="214" 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">
214
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<td class="diff-line-num new_line old" data-linenumber="0" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC214" class="line" lang="plaintext">ATGATGCGAGGTCGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACAGGAGTCGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTACATATCCTAATGCGCAGAGCCAATTCAGTCTGTGGCCGCAACAATGCGTATGTACCGGCAGGCTGGGACATTGTGTGTCAGCCGCATTCAAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCATGATCGCTATATCGAGACACCGACGAATTTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTACCTTTGGTCGCCGCACAGCCCGGCAACCCGGATGGCAGAAAAACTGTCAGCAACGCCTCCGCCTGGAGCGTGGCGCCGATGAGTTAACCGGAGAGTGATTTCGCCATTACTGGCCCGCCCCGCGGTGGTTGCCGGACTAGCAAGCAGATACGC</span>
</pre>
</td>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="plaintext">-.0..//--/,./0/./-..//-///.--202/1/..01/.01121011300400120434141102011131323/00201110/01100120200/12001././11///./..-.--240.-,....-.,-,--0/-.----+,,....,.,..,-,,--,,++,.--/2,,+/+,+,,-,.--..,,++-.-...----,-,/.1-/--,/+.--/-,+-++,,-,-/,,0---,+-...,---//.-.,,-----,,+,-/--,,-+------.,-,-..-/.,..-..,-,,-.-.,+.--,.../.,--0-,-,---..---...//....-.-./,--..----,/.12././,,/-,..0/--../0..././//..------+-.,..--....--,+,,.-.,.,--.,.,,,-2,,+,.++++**+**,*++0-,+++,+*)***++*.*)*,++</span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="plaintext">@54</span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="plaintext">GCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTATACCGCCCGCGCGGTGGTTGCCGACGCCCCGGACCGGCATACGC</span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="plaintext">//./././//...//1//..-..../-/--1//00//-...0/..----/././../--./.--.//...-../-,/,..-..-----/,-,-/,-.,--,./.,--..-.--.,-.+,1-,-,++-,,-.,+,++-+,+,,,,,,-,,</span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,7 +17,7 @@ namespace test {</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SpoaTest</span><span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">testing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Test</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"> <span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Setup</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">spoa</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">AlignmentType</span> <span class="n" style="color: #333;">type</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentType</span> <span class="n" style="color: #333;">type</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span> <span class="n" style="color: #333;">m</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span> <span class="n" style="color: #333;">g</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,9 +29,12 @@ class SpoaTest: public ::testing::Test {</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="mi" style="color: #099;">55</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">ae</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentEngine</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Create</span><span class="p">(</span><span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">gr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Graph</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">ae</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AlignmentEngine</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Create</span><span class="p">(</span><span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">gr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Graph</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">iq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">quality</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="p">}</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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Align</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">ms</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="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">ms</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,7 +43,7 @@ class SpoaTest: public ::testing::Test {</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ae</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">gr</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">quality</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">iq</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">AddAlignment</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quality</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">AddAlignment</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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">@@ -52,7 +55,19 @@ class SpoaTest: public ::testing::Test {</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">GenerateConsensus</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">msa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">GenerateMultipleSequenceAlignment</span><span class="p">();</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_TRUE</span><span class="p">(</span><span class="n" style="color: #333;">msa</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;">s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">msa</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">rs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">msa</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gc</span><span class="p">(</span><span class="n" style="color: #333;">rs</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">msa</span><span class="p">)</span> <span class="p">{</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">rs</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</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;">rs</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">gc</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</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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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="p">}</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="p">}</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">gc</span><span class="p">)</span> <span class="p">{</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_GT</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">it</span><span class="p">);</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="p">}</span></span>
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56
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"></span>
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57
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_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;">msa</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;">i</span><span class="p">)</span> <span class="p">{</span></span>
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58
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">msa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">msa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">),</span> <span class="n" style="color: #333;">msa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">());</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</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">@@ -61,13 +76,14 @@ class SpoaTest: public ::testing::Test {</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC78" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">biosoup</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Graph</span> <span class="n" style="color: #333;">gr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC79" 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;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AlignmentEngine</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ae</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">Graph</span> <span class="n" style="color: #333;">gr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">iq</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"><span class="n" style="color: #333;">TEST</span><span class="p">(</span><span class="n" style="color: #333;">SpoaAlignmentTest</span><span class="p">,</span> <span class="n" style="color: #333;">TypeError</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC85" 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="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">ae</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentEngine</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Create</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">ae</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AlignmentEngine</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Create</span><span class="p">(</span><span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">exception</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_STREQ</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">exception</span><span class="p">.</span><span class="n" style="color: #333;">what</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">@@ -76,24 +92,42 @@ TEST(SpoaAlignmentTest, TypeError) {</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"><span class="n" style="color: #333;">TEST</span><span class="p">(</span><span class="n" style="color: #333;">SpoaAlignmentTest</span><span class="p">,</span> <span class="n" style="color: #333;">EmptyInput</span><span class="p">)</span> <span class="p">{</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">ae</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">spoa</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">AlignmentEngine</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Create</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">spoa</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">spoa</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">Graph</span> <span class="n" style="color: #333;">g</span><span class="p">{};</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">ae</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">AlignmentEngine</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Create</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">Graph</span> <span class="n" style="color: #333;">g</span><span class="p">{};</span></span>
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81
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ae</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">);</span></span>
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82
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_TRUE</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">());</span></span>
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83
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"><span class="p">}</span></span>
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84
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"><span class="n" style="color: #333;">TEST</span><span class="p">(</span><span class="n" style="color: #333;">SpoaAlignmentTest</span><span class="p">,</span> <span class="n" style="color: #333;">LargeInput</span><span class="p">)</span> <span class="p">{</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">ae</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AlignmentEngine</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Create</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">ae</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Prealloc</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">exception</span><span class="p">)</span> <span class="p">{</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()).</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">11</span><span class="p">),</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="s" style="color: #d14;">"AlignmentEngine::Prealloc] error: too large sequence!"</span><span class="p">);</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="p">}</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">ae</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Prealloc</span><span class="p">((</span><span class="mi" style="color: #099;">1ULL</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">31</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">exception</span><span class="p">)</span> <span class="p">{</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" 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="p">(</span><span class="n" style="color: #333;">exception</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()).</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">11</span><span class="p">),</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="s" style="color: #d14;">"AlignmentEngine::Prealloc] error: insufficient memory!"</span><span class="p">);</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="p">}</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"><span class="p">}</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"></span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">Clear</span><span class="p">)</span> <span class="p">{</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">GenerateConsensus</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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91
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">GenerateConsensus</span><span class="p">());</span></span>
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93
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"><span class="p">}</span></span>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">Archive</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">spoa</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span 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="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span 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="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"></span>
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="p">{</span></span>
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133
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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;">ofstream</span> <span class="n" style="color: #333;">os</span><span class="p">(</span><span class="s" style="color: #d14;">"spoa.test.cereal"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,7 +136,7 @@ TEST_F(SpoaTest, Archive) {</td>
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102
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"> <span class="p">}</span></span>
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103
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"></span>
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104
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gr</span><span class="p">.</span><span class="n" style="color: #333;">GenerateConsensus</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">gr</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">Clear</span></span><span class="p"><span class="idiff right">()</span>;</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">gr</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{}</span>;</span></span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"></span>
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107
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="p">{</span></span>
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108
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142
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<pre style="margin: 0;"> <span id="LC142" 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;">ifstream</span> <span class="n" style="color: #333;">is</span><span class="p">(</span><span class="s" style="color: #d14;">"spoa.test.cereal"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" 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="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">@@ -114,7 +148,8 @@ TEST_F(SpoaTest, Archive) {</td>
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114
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"><span class="p">}</span></span>
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115
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"></span>
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116
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">Local</span><span class="p">)</span> <span class="p">{</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"></span>
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154
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<pre style="margin: 0;"> <span id="LC154" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"> <span class="s" style="color: #d14;">"AATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGAC"</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -129,7 +164,8 @@ TEST_F(SpoaTest, Local) {</td>
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129
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"><span class="p">}</span></span>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"></span>
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131
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">LocalAffine</span><span class="p">)</span> <span class="p">{</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"></span>
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170
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<pre style="margin: 0;"> <span id="LC170" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"> <span class="s" style="color: #d14;">"AATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGAC"</span></span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="180" 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">@@ -144,7 +180,8 @@ TEST_F(SpoaTest, LocalAffine) {</td>
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144
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp"><span class="p">}</span></span>
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145
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"></span>
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">LocalConvex</span><span class="p">)</span> <span class="p">{</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"></span>
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149
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186
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<pre style="margin: 0;"> <span id="LC186" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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150
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp"> <span class="s" style="color: #d14;">"AATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGAC"</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -159,7 +196,8 @@ TEST_F(SpoaTest, LocalConvex) {</td>
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159
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"><span class="p">}</span></span>
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160
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp"></span>
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161
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">LocalWithQualities</span><span class="p">)</span> <span class="p">{</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"></span>
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164
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202
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<pre style="margin: 0;"> <span id="LC202" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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165
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"> <span class="s" style="color: #d14;">"AATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGAC"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="174" 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="212" 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">@@ -174,7 +212,8 @@ TEST_F(SpoaTest, LocalWithQualities) {</td>
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174
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"><span class="p">}</span></span>
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175
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"></span>
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176
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">LocalAffineWithQualities</span><span class="p">)</span> <span class="p">{</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"></span>
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218
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<pre style="margin: 0;"> <span id="LC218" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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180
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp"> <span class="s" style="color: #d14;">"AATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGAC"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -189,7 +228,8 @@ TEST_F(SpoaTest, LocalAffineWithQualities) {</td>
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189
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"><span class="p">}</span></span>
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190
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp"></span>
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191
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">LocalConvexWithQualities</span><span class="p">)</span> <span class="p">{</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kSW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"></span>
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234
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<pre style="margin: 0;"> <span id="LC234" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="s" style="color: #d14;">"AATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGAC"</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="244" 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">@@ -204,7 +244,8 @@ TEST_F(SpoaTest, LocalConvexWithQualities) {</td>
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204
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"><span class="p">}</span></span>
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205
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"></span>
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">Global</span><span class="p">)</span> <span class="p">{</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"></span>
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209
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250
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<pre style="margin: 0;"> <span id="LC250" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACA"</span></span>
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<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">@@ -219,7 +260,8 @@ TEST_F(SpoaTest, Global) {</td>
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219
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"><span class="p">}</span></span>
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"></span>
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">GlobalAffine</span><span class="p">)</span> <span class="p">{</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"></span>
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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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACA"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="234" 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="276" 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">@@ -234,7 +276,8 @@ TEST_F(SpoaTest, GlobalAffine) {</td>
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234
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"><span class="p">}</span></span>
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235
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"></span>
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">GlobalConvex</span><span class="p">)</span> <span class="p">{</span></span>
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237
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp"></span>
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282
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<pre style="margin: 0;"> <span id="LC282" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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240
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACA"</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="292" 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">@@ -249,7 +292,8 @@ TEST_F(SpoaTest, GlobalConvex) {</td>
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249
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"><span class="p">}</span></span>
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp"></span>
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">GlobalWithQualities</span><span class="p">)</span> <span class="p">{</span></span>
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252
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"></span>
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298
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<pre style="margin: 0;"> <span id="LC298" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACA"</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="308" 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">@@ -264,7 +308,8 @@ TEST_F(SpoaTest, GlobalWithQualities) {</td>
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264
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cpp"><span class="p">}</span></span>
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265
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"></span>
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">GlobalAffineWithQualities</span><span class="p">)</span> <span class="p">{</span></span>
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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;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"></span>
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314
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<pre style="margin: 0;"> <span id="LC314" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACA"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="279" 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="324" 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">@@ -279,7 +324,8 @@ TEST_F(SpoaTest, GlobalAffineWithQualities) {</td>
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279
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"><span class="p">}</span></span>
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"></span>
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">GlobalConvexWithQualities</span><span class="p">)</span> <span class="p">{</span></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kNW</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp"></span>
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330
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<pre style="margin: 0;"> <span id="LC330" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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285
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACA"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="294" 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="340" 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">@@ -294,7 +340,8 @@ TEST_F(SpoaTest, GlobalConvexWithQualities) {</td>
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294
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"><span class="p">}</span></span>
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295
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="cpp"></span>
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296
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">SemiGlobal</span><span class="p">)</span> <span class="p">{</span></span>
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297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kOV</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kOV</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"></span>
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346
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<pre style="margin: 0;"> <span id="LC346" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ACATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGA"</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="356" 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">@@ -309,7 +356,8 @@ TEST_F(SpoaTest, SemiGlobal) {</td>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"></span>
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">SemiGlobalAffine</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kOV</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kOV</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"></span>
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362
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<pre style="margin: 0;"> <span id="LC362" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="cpp"> <span class="s" style="color: #d14;">"GTATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGA"</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">@@ -324,7 +372,8 @@ TEST_F(SpoaTest, SemiGlobalAffine) {</td>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cpp"><span class="p">}</span></span>
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">SemiGlobalConvex</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kOV</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kOV</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp"></span>
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378
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<pre style="margin: 0;"> <span id="LC378" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"> <span class="s" style="color: #d14;">"GTATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGA"</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="388" 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">@@ -339,7 +388,8 @@ TEST_F(SpoaTest, SemiGlobalConvex) {</td>
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"><span class="p">}</span></span>
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp"></span>
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341
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">SemiGlobalWithQualities</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kOV</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kOV</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"></span>
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394
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<pre style="margin: 0;"> <span id="LC394" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ACATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGA"</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">@@ -354,7 +404,8 @@ TEST_F(SpoaTest, SemiGlobalWithQualities) {</td>
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354
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="cpp"><span class="p">}</span></span>
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355
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"></span>
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">SemiGlobalAffineWithQualities</span><span class="p">)</span> <span class="p">{</span></span>
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357
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kOV</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kOV</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cpp"></span>
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410
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<pre style="margin: 0;"> <span id="LC410" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ACATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGA"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -369,7 +420,8 @@ TEST_F(SpoaTest, SemiGlobalAffineWithQualities) {</td>
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369
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"><span class="p">}</span></span>
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370
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421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="cpp"></span>
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371
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422
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">SpoaTest</span><span class="p">,</span> <span class="n" style="color: #333;">SemiGlobalConvexWithQualities</span><span class="p">)</span> <span class="p">{</span></span>
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372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">spoa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kOV</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <span class="n" style="color: #333;">Setup</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kOV</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">Align</span><span class="p">();</span></span>
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp"></span>
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374
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426
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<pre style="margin: 0;"> <span id="LC426" 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;">c</span> <span class="o" style="font-weight: 600;">=</span></span>
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375
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427
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cpp"> <span class="s" style="color: #d14;">"GTATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGA"</span></span>
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