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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/diamond-aligner">Debian Med / diamond-aligner</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d">81c84b01</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-16T16:20:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.14</pre>
</li>
</ul>
<h4>17 changed files:</h4>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="new-file">
+
.travis.yml
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</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#ba308c53c268704c3008f5e2e6e8129f9f6bf3fe">
src/ChangeLog
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<li class="file-stats">
<a href="#76d5a97c09cca591280144de40f9c04a5ec57ef7">
src/basic/basic.cpp
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<li class="file-stats">
<a href="#da280a51d91809345347036c4e31920b2c744ab7">
src/basic/const.h
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<li class="file-stats">
<a href="#503a0d0a04d792d79a548b340f7e1a9201a8d375">
src/dp/score_vector_int16.h
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<li class="file-stats">
<a href="#fca48027490c3c37433bb7bfe054875f42886c49">
src/dp/score_vector_int8.h
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<li class="file-stats">
<a href="#36c9568495b5e92087ac3999322cf44d3d5cda7d">
src/dp/swipe/banded_3frame_swipe.cpp
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<li class="file-stats">
<a href="#3895b3c92f5954d61a368fe229b92c15caa8177d">
src/dp/swipe/banded_swipe.h
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<li class="file-stats">
<a href="#f22dbb432f34ebbde855082d0b3934c8d73c1daf">
src/dp/swipe/full_swipe.h
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<li class="file-stats">
<a href="#f029c9266faec97f105981cc4f88e78d3b78027b">
src/dp/swipe/swipe.h
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<li class="file-stats">
<a href="#e744f4de2bef9a2b087868b317337a012d7e61ce">
src/output/blast_tab_format.cpp
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<li class="file-stats">
<a href="#aa259442e19873ad55a6f52ffa51a238a63c79d3">
src/test/test_cases.cpp
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<li class="file-stats">
<a href="#3062314bb150f152af7ac80cd0fca55e311e2fc5">
src/tools/benchmark.cpp
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<li class="file-stats">
<a href="#4782c94b104195c88cf9d55c59c0dd7053bf7ab8">
src/tools/benchmark_swipe.cpp
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<li class="file-stats">
<a href="#45027e1590ce8ffdb47fb619b29662f817a3ccf2">
src/util/simd.h
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<li class="file-stats">
<a href="#2ec7dc43068fc79fd78773238616dba736db6015">
src/util/system/system.cpp
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</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">os</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">osx</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - xenial</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">trusty</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">c++</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#addons:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># apt:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># packages:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - gdb</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - libclang-common-6.0-dev</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"><span class="na" style="color: #008080;">arch</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">amd64</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">arm64</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ppc64le</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">s390x</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"><span class="na" style="color: #008080;">compiler</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - clang</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span> <span class="s" style="color: #d14;">skip</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir build</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd build</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake -DCMAKE_BUILD_TYPE=Release ..</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - gdb --ex=r -return-child-result -batch -ex bt --args ./diamond test</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - lldb --batch --one-line r --one-line-on-crash bt -- ./diamond test</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./diamond test</span></span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</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">@@ -116,13 +116,16 @@ set(DISPATCH_OBJECTS</td>
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cmake"><span class="s2" style="color: #d14;">"src/dp/swipe/banded_3frame_swipe.cpp"</span></span>
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cmake"><span class="s2" style="color: #d14;">"src/search/stage2.cpp"</span></span>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cmake"><span class="s2" style="color: #d14;">"src/tools/benchmark.cpp"</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cmake"><span class="s2" style="color: #d14;">"src/tools/benchmark_swipe.cpp"</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cmake"><span class="s2" style="color: #d14;">"src/dp/swipe/swipe_wrapper.cpp"</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cmake"><span class="s2" style="color: #d14;">"src/util/tantan.cpp"</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cmake"><span class="s2" style="color: #d14;">"src/dp/scan_diags.cpp"</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cmake"><span class="s2" style="color: #d14;">"src/dp/ungapped_simd.cpp"</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cmake"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cmake"></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>EXTRA<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">LIST</span><span class="p">(</span>APPEND DISPATCH_OBJECTS <span class="s2" style="color: #d14;">"src/tools/benchmark_swipe.cpp"</span><span class="p">)</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" 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="LC128" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_library</span><span class="p">(</span>arch_generic OBJECT <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">DISPATCH_OBJECTS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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127
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_compile_options</span><span class="p">(</span>arch_generic PUBLIC -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC<span class="p">)</span></span>
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128
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_include_directories</span><span class="p">(</span>arch_generic PRIVATE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/src/lib"</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#ba308c53c268704c3008f5e2e6e8129f9f6bf3fe"><strong>src/ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[2.0.14]</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- Fixed a compiler error on Linux systems that do not define `_SC_LEVEL3_CACHE_SIZE`.</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">- Fixed an error when using `--unal 1` with the `cigar` output field.</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">- Fixed an `illegal instruction` error on systems that did not support AVX2.</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">- Fixed a bug (present since v2.0.12) that could cause an error or suboptimal</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> alignments when HSP filter settings were used.</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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1
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">[2.0.13]</span>
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2
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">- Fixed a bug that caused invalid bit scores in frameshift alignment mode.</span>
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3
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#76d5a97c09cca591280144de40f9c04a5ec57ef7"><strong>src/basic/basic.cpp</strong></a>
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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>
<td class="diff-line-num unfold js-unfold new_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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +29,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.</td>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../util/util.h"</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../stats/standard_matrix.h"</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;">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;">Const</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">version_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.0.1<span class="idiff left right">3</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" 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;">Const</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">version_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.0.1<span class="idiff left right">4</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="k" style="font-weight: 600;">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;">Const</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"diamond"</span><span class="p">;</span></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="LC35" class="line" lang="cpp"><span class="n" style="color: #333;">Align_mode</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Align_mode</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">mode</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#da280a51d91809345347036c4e31920b2c744ab7"><strong>src/basic/const.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,7 +25,7 @@ struct Const</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"> <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"> <span class="n" style="color: #333;">build_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15<span class="idiff left right">1</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"> <span class="n" style="color: #333;">build_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15<span class="idiff left right">2</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef SINGLE_THREADED</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"> <span class="n" style="color: #333;">seedp_bits</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="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#503a0d0a04d792d79a548b340f7e1a9201a8d375"><strong>src/dp/score_vector_int16.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -206,30 +206,9 @@ struct ScoreVector<int16_t, DELTA></td>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">data_</span><span class="p">(</span><span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">x</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">ScoreVector</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">row</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</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;">score_matrix</span><span class="p">.</span><span class="n" style="color: #333;">matrix16</span><span class="p">()[</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">5</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xff</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</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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<pre style="margin: 0;">-<span id="LC214" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">|=</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xff</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">16</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</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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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">|=</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xff</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">16</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</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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<pre style="margin: 0;">-<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">|=</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xff</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">16</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</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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<pre style="margin: 0;">-<span id="LC220" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xff</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</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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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">|=</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xff</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">16</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</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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<pre style="margin: 0;">-<span id="LC224" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">|=</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xff</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">16</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</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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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">|=</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xff</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">16</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cpp"> <span class="n" style="color: #333;">data_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_set_epi64x</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __SSSE3__</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">ScoreVector</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">Register</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __SSSE3__</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128i</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;">score_matrix</span><span class="p">.</span><span class="n" style="color: #333;">matrix8u</span><span class="p">()[</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">5</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"></span>
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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;">__m128i</span> <span class="n" style="color: #333;">high_mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_epi16</span><span class="p">(</span><span class="n" style="color: #333;">_mm_and_si128</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SIMD</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mm_set1_epi8</span><span class="p">(</span><span class="sc" style="color: #d14;">'\x10'</span><span class="p">)),</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="242" 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="221" 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">@@ -242,8 +221,8 @@ struct ScoreVector<int16_t, DELTA></td>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">__m128i</span> <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_shuffle_epi8</span><span class="p">(</span><span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="n" style="color: #333;">seq_high</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">data_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si128</span><span class="p">(</span><span class="n" style="color: #333;">_mm_or_si128</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span><span class="p">),</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SIMD</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mm_set1_epi16</span><span class="p">(</span><span class="mi" style="color: #099;">255</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">data_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_subs_epi16</span><span class="p">(</span><span class="n" style="color: #333;">data_</span><span class="p">,</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SIMD</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_mm_set1_epi16</span><span class="p">(</span><span class="n" style="color: #333;">score_matrix</span><span class="p">.</span><span class="n" style="color: #333;">bias</span><span class="p">()));</span></span>
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<pre style="margin: 0;">-<span id="LC245" 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="LC224" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC225" 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="LC226" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp"> <span class="n" style="color: #333;">ScoreVector</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">+</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreVector</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rhs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#fca48027490c3c37433bb7bfe054875f42886c49"><strong>src/dp/score_vector_int8.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="238" 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">@@ -238,6 +238,7 @@ struct ScoreVector<int8_t, DELTA></td>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="n" style="color: #333;">data_</span><span class="p">(</span><span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">(</span><span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"> <span class="p">{</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __SSSE3__</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">ScoreVector</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">__m128i</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128i</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;">score_matrix</span><span class="p">.</span><span class="n" style="color: #333;">matrix8</span><span class="p">()[</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">5</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">@@ -252,6 +253,7 @@ struct ScoreVector<int8_t, DELTA></td>
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252
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"> <span class="n" style="color: #333;">__m128i</span> <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_shuffle_epi8</span><span class="p">(</span><span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="n" style="color: #333;">seq_high</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">data_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_or_si128</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC256" 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="LC257" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="n" style="color: #333;">ScoreVector</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">+</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreVector</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rhs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"> <span class="p">{</span></span>
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<li id="36c9568495b5e92087ac3999322cf44d3d5cda7d">
<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#36c9568495b5e92087ac3999322cf44d3d5cda7d"><strong>src/dp/swipe/banded_3frame_swipe.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">@@ -425,6 +425,7 @@ list<Hsp> banded_3frame_swipe(</td>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp"> <span class="n" style="color: #333;">frameshift_penalty</span><span class="p">(</span><span class="n" style="color: #333;">score_matrix</span><span class="p">.</span><span class="n" style="color: #333;">frame_shift</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cpp"> <span class="n" style="color: #333;">SwipeProfile</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">_sv</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">profile</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC428" 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;">array</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="mi" style="color: #099;">32</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">target_scores</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"> <span class="n" style="color: #333;">Score</span> <span class="n" style="color: #333;">best</span><span class="p">[</span><span class="n" style="color: #333;">ScoreTraits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">_sv</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">CHANNELS</span><span class="p">];</span></span>
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_col</span><span class="p">[</span><span class="n" style="color: #333;">ScoreTraits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">_sv</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">CHANNELS</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ScoreTraits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">_sv</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">CHANNELS</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -443,7 +444,11 @@ list<Hsp> banded_3frame_swipe(</td>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="cpp"> <span class="n" style="color: #333;">_sv</span> <span class="n" style="color: #333;">vgap0</span><span class="p">,</span> <span class="n" style="color: #333;">vgap1</span><span class="p">,</span> <span class="n" style="color: #333;">vgap2</span><span class="p">,</span> <span class="n" style="color: #333;">hgap</span><span class="p">,</span> <span class="n" style="color: #333;">col_best</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;">vgap0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vgap1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vgap2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">col_best</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ScoreTraits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">_sv</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">zero</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __SSSE3__</span></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp"> <span class="n" style="color: #333;">profile</span><span class="p">.</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;">targets</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"> <span class="n" style="color: #333;">profile</span><span class="p">.</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;">targets</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">target_scores</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">()));</span></span>
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<pre style="margin: 0;">+<span id="LC451" 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="LC452" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i0_</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;">i1_</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="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">hgap</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;">hgap</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp"> <span class="n" style="color: #333;">_sv</span> <span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cell_update</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">_sv</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">.</span><span class="n" style="color: #333;">sm3</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="p">.</span><span class="n" style="color: #333;">sm4</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="p">.</span><span class="n" style="color: #333;">sm2</span><span class="p">,</span> <span class="n" style="color: #333;">profile</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]),</span> <span class="n" style="color: #333;">extend_penalty</span><span class="p">,</span> <span class="n" style="color: #333;">open_penalty</span><span class="p">,</span> <span class="n" style="color: #333;">frameshift_penalty</span><span class="p">,</span> <span class="n" style="color: #333;">hgap</span><span class="p">,</span> <span class="n" style="color: #333;">vgap0</span><span class="p">,</span> <span class="n" style="color: #333;">col_best</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#3895b3c92f5954d61a368fe229b92c15caa8177d"><strong>src/dp/swipe/banded_swipe.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -97,14 +97,16 @@ Hsp traceback(_cbs bias_correction, const Matrix<Cell> &dp, const DpTarget &targ</td>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">bit_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score_matrix</span><span class="p">.</span><span class="n" style="color: #333;">bitscore</span><span class="p">(</span><span class="n" style="color: #333;">out</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="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">frame</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">frame</span><span class="p">.</span><span class="n" style="color: #333;">index</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;">out</span><span class="p">.</span><span class="n" style="color: #333;">matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">matrix</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;">out</span><span class="p">.</span><span class="n" style="color: #333;">d_begin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">d_begin</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">d_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">d_end</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i1</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">d_end</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;">i1_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">max_col</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">max_band_i</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;">j1_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">max_col</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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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">carry_over</span><span class="p">.</span><span class="n" style="color: #333;">i1</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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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">d_begin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">d_begin</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;">out</span><span class="p">.</span><span class="n" style="color: #333;">d_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">d_end</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="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">query_range</span><span class="p">.</span><span class="n" style="color: #333;">end_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i1_</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="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">subject_range</span><span class="p">.</span><span class="n" style="color: #333;">end_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j1_</span><span class="p">;</span></span>
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106
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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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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</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;">out</span><span class="p">.</span><span class="n" style="color: #333;">d_begin</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">d_end</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">length</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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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">d_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">d_begin</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">length</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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108
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">query_range</span><span class="p">.</span><span class="n" style="color: #333;">end_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">carry_over</span><span class="p">.</span><span class="n" style="color: #333;">i1</span><span class="p">;</span></span>
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109
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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;">out</span><span class="p">.</span><span class="n" style="color: #333;">subject_range</span><span class="p">.</span><span class="n" style="color: #333;">end_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">carry_over</span><span class="p">.</span><span class="n" style="color: #333;">j1</span><span class="p">;</span></span>
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110
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">identities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">carry_over</span><span class="p">.</span><span class="n" style="color: #333;">ident</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="252" 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="254" 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">@@ -252,7 +254,11 @@ list<Hsp> swipe(const vector<DpTarget>::const_iterator subject_begin, const vect</td>
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252
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">profile</span><span class="p">.</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;">targets</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">target_scores</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">()));</span></span>
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253
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"> <span class="p">}</span></span>
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254
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<td class="new_line diff-line-num" data-linenumber="256" 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">
256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __SSSE3__</span></span>
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255
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="n" style="color: #333;">profile</span><span class="p">.</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;">target_seqv</span><span class="p">);</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="n" style="color: #333;">profile</span><span class="p">.</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;">targets</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">target_scores</span><span class="p">.</span><span class="n" style="color: #333;">data</span><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 class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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256
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"> <span class="p">}</span></span>
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257
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DP_STAT</span></span>
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258
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">live</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targets</span><span class="p">.</span><span class="n" style="color: #333;">live</span><span class="p">();</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#f22dbb432f34ebbde855082d0b3934c8d73c1daf"><strong>src/dp/swipe/full_swipe.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -162,7 +162,11 @@ list<Hsp> swipe(const It target_begin, const It target_end, std::atomic_size_t*</td>
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162
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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;">profile</span><span class="p">.</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;">targets</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">target_scores</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">()));</span></span>
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163
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="p">}</span></span>
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164
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <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 class="cp" style="color: #999; font-weight: 600;">#ifdef __SSSE3__</span></span>
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165
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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;">profile</span><span class="p">.</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;">target_seq_vector</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="cp" style="color: #999; font-weight: 600;">#else</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;">profile</span><span class="p">.</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;">targets</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">target_scores</span><span class="p">.</span><span class="n" style="color: #333;">data</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 class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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166
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <span class="p">}</span></span>
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167
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"></span>
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168
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DP_STAT</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#f029c9266faec97f105981cc4f88e78d3b78027b"><strong>src/dp/swipe/swipe.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" 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">@@ -92,12 +92,14 @@ template<typename Sv></td>
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92
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">SwipeProfile</span></span>
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93
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"><span class="p">{</span></span>
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94
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __SSSE3__</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">set</span><span class="p">(</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">ScoreTraits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sv</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Vector</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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96
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="p">{</span></span>
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97
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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;">assert</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">data_</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;">Sv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">value_traits</span><span class="p">.</span><span class="n" style="color: #333;">alphabet_size</span><span class="p">);</span></span>
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98
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">AMINO_ACID_COUNT</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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99
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">data_</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;">Sv</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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100
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <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="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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101
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"></span>
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102
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="kr" style="font-weight: 600;">inline</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sv</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">Letter</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</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>
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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">@@ -166,7 +168,7 @@ struct SwipeProfile<int32_t></td>
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166
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">32</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>
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167
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">row</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;">target_scores</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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168
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <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 class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">set</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;"><span class="idiff right">*</span></span><span class="n" style="color: #333;">target_scores</span><span class="p">)</span> <span class="p">{</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">set</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span>*</span> <span class="n" style="color: #333;">target_scores</span><span class="p">)</span> <span class="p">{</span></span>
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170
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">32</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>
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171
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">row</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;">target_scores</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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172
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#e744f4de2bef9a2b087868b317337a012d7e61ce"><strong>src/output/blast_tab_format.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">@@ -489,6 +489,7 @@ void Blast_tab_format::print_query_intro(size_t query_num, const char *query_nam</td>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">55</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">56</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">57</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">58</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">59</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">60</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">63</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#aa259442e19873ad55a6f52ffa51a238a63c79d3"><strong>src/test/test_cases.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">@@ -66,7 +66,7 @@ const vector<uint64_t> ref_hashes = {</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"><span class="mh" style="color: #099;">0xe787dcb23cc5b120</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"><span class="mh" style="color: #099;">0x5aa4baf48a888be9</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="mh" style="color: #099;">0xa2519e06e3bfa2fd</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"><span class="mh" style="color: #099;">0x<span class="idiff left right">1edd906017a3ddb</span>2</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"><span class="mh" style="color: #099;">0x<span class="idiff left right">c393e16a2f78256</span>2</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><span class="mh" style="color: #099;">0x67b3a14cdd541dc3</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#3062314bb150f152af7ac80cd0fca55e311e2fc5"><strong>src/tools/benchmark.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">@@ -55,7 +55,7 @@ using namespace DISPATCH_ARCH;</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">Benchmark</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">DISPATCH_ARCH</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="cp" style="color: #999; font-weight: 600;">#ifdef<span class="idiff left right"> </span>__SSE4_1__</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if<span class="idiff left"> </span>def<span class="idiff">ined(</span>__SSE4_1__<span class="idiff right">) && defined(EXTRA)</span></span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">swipe_cell_update</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC60" 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="LC61" 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">@@ -327,7 +327,7 @@ void matrix_adjust(const Sequence& s1, const Sequence& s2) {</td>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">benchmark</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"swipe"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef<span class="idiff left right"> </span>__SSE4_1__</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if<span class="idiff left"> </span>def<span class="idiff">ined(</span>__SSE4_1__<span class="idiff right">) && defined(EXTRA)</span></span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp"> <span class="n" style="color: #333;">swipe_cell_update</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC332" 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="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#4782c94b104195c88cf9d55c59c0dd7053bf7ab8"><strong>src/tools/benchmark_swipe.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">@@ -20,12 +20,10 @@ static const size_t N = 256;</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">Sv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ScoreVector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="p">,</span> <span class="n" style="color: #333;">SCHAR_MIN</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">Cell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ForwardCell</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sv</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//using Cell = Sv;</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Cell</span> <span class="n" style="color: #333;">diagonal_cell</span><span class="p">[</span><span class="n" style="color: #333;">N</span><span class="p">],</span> <span class="n" style="color: #333;">horizontal_gap</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="LC23" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">query</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="LC25" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Sv</span> <span class="n" style="color: #333;">profile</span><span class="p">[</span><span class="mi" style="color: #099;">32</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">C</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ScoreTraits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sv</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">CHANNELS</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">update_row</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">update_row</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Cell</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">diagonal_cell</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Cell</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">horizontal_gap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Sv</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 right">profile</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//auto id_mask = DummyIdMask<Sv>(0, Sv());</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">id_mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VectorIdMask</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sv</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">Sv</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//auto row_counter = DummyRowCounter(0);</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">@@ -41,6 +39,8 @@ static void update_row() {</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">swipe_cell_update</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>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000000llu</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;">Cell</span> <span class="n" style="color: #333;">diagonal_cell</span><span class="p">[</span><span class="n" style="color: #333;">N</span><span class="p">],</span> <span class="n" style="color: #333;">horizontal_gap</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="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">Sv</span> <span class="n" style="color: #333;">profile</span><span class="p">[</span><span class="mi" style="color: #099;">32</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">N</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="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">query</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;">rand</span><span class="p">()</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC46" 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">@@ -53,7 +53,7 @@ void swipe_cell_update() {</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">high_resolution_clock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">time_point</span> <span class="n" style="color: #333;">t1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">high_resolution_clock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">now</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</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="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">update_row</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;">update_row</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">diagonal_cell</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">horizontal_gap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">profile</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">volatile</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diagonal_cell</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">data_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">volatile</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diagonal_cell</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">ident</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#45027e1590ce8ffdb47fb619b29662f817a3ccf2"><strong>src/util/simd.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,7 +102,9 @@ static inline __m256i _mm256_set1_epi16(short v) {</td>
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102
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"><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>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(__GNUC__) && __GNUC__ < 8</span></span>
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105
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define _mm256_set_m128i(v0, v1) _mm256_insertf128_si256(_mm256_castsi128_si256(v1), (v0), 1)</span></span>
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<pre style="margin: 0;">+<span id="LC107" 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="LC108" class="line" lang="cpp"></span>
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107
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">print_8</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span> <span class="n" style="color: #333;">x</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;">ostream</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="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">alignas</span><span class="p">(</span><span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="kt" style="color: #458; font-weight: 600;">int8_t</span> <span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">32</span><span class="p">];</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/81c84b01fab3558d2e53b11e1fddbccd2701c12d#2ec7dc43068fc79fd78773238616dba736db6015"><strong>src/util/system/system.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">@@ -192,7 +192,7 @@ void unmap_file(char* ptr, size_t size, int fd) {</td>
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"><span class="p">}</span></span>
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="nf" style="color: #900; font-weight: 600;">l3_cache_size</span><span class="p">()</span> <span class="p">{</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(_MSC_VER) || defined(__APPLE__) || defined(__FreeBSD__)</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(_MSC_VER) || defined(__APPLE__) || defined(__FreeBSD__)<span class="idiff left right"> || (! defined(_SC_LEVEL3_CACHE_SIZE))</span></span></span>
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196
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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197
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sysconf</span><span class="p">(</span><span class="n" style="color: #333;">_SC_LEVEL3_CACHE_SIZE</span><span class="p">);</span></span>
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