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<h3>
Steffen Möller 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/30dedeaf53a7c61254b0a923de683bb50b14fc30">30dedeaf</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-09-19T22:20:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.9.26+dfsg</pre>
</li>
</ul>
<h4>29 changed files:</h4>
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#32d9e95f00ee666c09c6aa675993f5e25887ecaa">
build_simple.sh
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<li class="file-stats">
<a href="#ba308c53c268704c3008f5e2e6e8129f9f6bf3fe">
src/ChangeLog
</a>
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<li class="file-stats">
<a href="#c8d7bd122d50035cfb1627dbd9659f00b8137ded">
src/align/banded_swipe_pipeline.cpp
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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="#fe8c534c15ea9cf93547993244c3ab903c4895ff">
src/basic/config.cpp
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<li class="file-stats">
<a href="#79a175a8b141cc4f06683108fcd39b79a555f1cd">
src/basic/config.h
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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="#992408bab41b605763e629e7a719178aef609bae">
src/basic/masking.cpp
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<li class="file-stats">
<a href="#e64142605ff8612313a434ebbb47a669146a4d86">
src/basic/masking.h
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<li class="file-stats">
<a href="#bb140dcc3945bad51e678d633d41915c87344b2f">
src/data/ref_dictionary.cpp
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<li class="file-stats">
<a href="#4c75bd371ff8a5ac8f8c6c03800a0d197a6baf78">
src/data/reference.cpp
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<li class="file-stats">
<a href="#b4ebfd635f4bc15a73d7a817b3af743fc2daf57a">
src/data/reference.h
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<li class="file-stats">
<a href="#8366fdef1b3e7c06b4325bf704ef6a9a25477168">
src/data/seed_array.cpp
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<li class="file-stats">
<a href="#4d74b3b7d5a1f59aa02245bde00681d093e8d8a3">
src/data/seed_array.h
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<li class="file-stats">
<a href="#79ac9d06e448a7f7da92ca7130fc5d7818aaf460">
src/dp/needleman_wunsch.cpp
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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="#61f8e8d714778e5355aa05d2be26c9fef3c4f128">
<span class="new-file">
+
src/lib/tantan/LambdaCalculator.cc
</span>
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<li class="file-stats">
<a href="#a0592a74c753eee83c242399a07f04bbb888f2f1">
<span class="new-file">
+
src/lib/tantan/LambdaCalculator.hh
</span>
</a>
</li>
<li class="file-stats">
<a href="#7d9733b309ffca9c00e603bbc75bdef36b121081">
src/run/cluster.cpp
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<li class="file-stats">
<a href="#aa612a337fc66ae885c76e4eb2a819dfd69117f8">
src/run/double_indexed.cpp
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<li class="file-stats">
<a href="#bd735448b4c157cfe3470c9dca2a5f97ef2682db">
src/run/tools.cpp
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<li class="file-stats">
<a href="#d617200d9067f8f78c9396cbc28dc9307c8738cd">
src/util/command_line_parser.cpp
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<li class="file-stats">
<a href="#c594ddd20c4c5befe842e4f70eccdc1934b9a261">
src/util/io/file_backed_buffer.h
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<li class="file-stats">
<a href="#1f1991a4cdd1bf9ed0a3e3d9cfa2018c12da9246">
src/util/io/input_file.cpp
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<li class="file-stats">
<a href="#2370dc5cead55336c866ff7109bc5eaaa392a9d0">
src/util/io/input_file.h
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<li class="file-stats">
<a href="#d7cc4906956f41fd1ab5a474f924cefcaca5c537">
src/util/io/temp_file.cpp
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<li class="file-stats">
<a href="#c6904c8405257ade3a64d5717e7b3e7ca86c2f4e">
src/util/io/temp_file.h
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</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -149,6 +149,7 @@ add_executable(diamond src/run/main.cpp</td>
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149
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cmake"> src/tools/tools.cpp</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
150
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC150" class="line" lang="cmake"> src/util/system/getRSS.cpp</span>
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<td class="diff-line-num old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
151
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC151" class="line" lang="cmake"> src/util/math/sparse_matrix.cpp</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC152" class="line" lang="cmake"> src/lib/tantan/LambdaCalculator.cc</span>
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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
153
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC153" class="line" lang="cmake"><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
153
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<td class="diff-line-num new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
154
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC154" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
154
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<td class="diff-line-num new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
155
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC155" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>EXTRA<span class="p">)</span></span>
</pre>
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</table>
<br>
</li>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="21" 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">@@ -21,11 +21,6 @@ Keep posted about new developments by following me on</td>
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<td class="diff-line-num old_line" data-linenumber="21" 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">
21
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">image</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/diamond/badges/platforms.svg</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="22" 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">
22
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<td class="diff-line-num new_line" data-linenumber="22" 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">
22
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![image</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/diamond/badges/downloads.svg</span><span class="p">)</span>](https://anaconda.org/bioconda/diamond)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="23" 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">
23
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<td class="diff-line-num new_line" data-linenumber="23" 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">
23
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Support</span></span>
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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=======</span></span>
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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown">The preferred support channel is the <span class="p">[</span><span class="nv" style="color: #008080;">Diamond community website</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.diamondsearch.org/</span><span class="p">)</span>. It provides a platform for users to exchange their experiences and get support directly from the developer. You may also use the GitHub issue tracker or send inquiries by email.</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Quick start guide</span></span>
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30
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=================</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" 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="32" 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">@@ -37,7 +32,7 @@ quick example for setting up and using the program on Linux.</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown">Installing the software on your system may be done by downloading it in</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown">binary format for immediate use:</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"><span class="sb" style="color: #d14;"> wget http://github.com/bbuchfink/diamond/releases/download/v0.9.2<span class="idiff left right">5</span>/diamond-linux64.tar.gz</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="sb" style="color: #d14;"> wget http://github.com/bbuchfink/diamond/releases/download/v0.9.2<span class="idiff left right">6</span>/diamond-linux64.tar.gz</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="sb" style="color: #d14;"> tar xzf diamond-linux64.tar.gz</span></span>
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42
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown">The extracted <span class="sb" style="color: #d14;">`diamond`</span> binary file should be moved to a directory</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" 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="73" 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">@@ -78,6 +73,11 @@ The output file here is specified with the `–o` option and named</td>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"><span class="p">-</span> The default e-value cutoff of DIAMOND is 0.001 while that of</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown"> BLAST is 10, so by default the program will search a lot more</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="markdown"> stringently than BLAST and not report weak hits.</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Support</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=======</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown">The preferred support channel is the <span class="p">[</span><span class="nv" style="color: #008080;">Diamond community website</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.diamondsearch.org/</span><span class="p">)</span>. It provides a platform for users to exchange their experiences and get support directly from the developer. You may also use the GitHub issue tracker or send inquiries by email.</span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"> </span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">About</span></span>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=====</span></span>
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<br>
</li>
<li id="32d9e95f00ee666c09c6aa675993f5e25887ecaa">
<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#32d9e95f00ee666c09c6aa675993f5e25887ecaa"><strong>build_simple.sh</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="81" 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="81" 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">@@ -81,4 +81,5 @@ g++ -std=gnu++11 -DNDEBUG -O3 -Wno-deprecated-declarations $1 $2 $3 \</td>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="shell"> src/tools/tools.cpp <span class="se" style="color: #d14;">\</span></span>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="shell"> src/util/system/getRSS.cpp <span class="se" style="color: #d14;">\</span></span>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="shell"> src/util/math/sparse_matrix.cpp <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"> src/lib/tantan/LambdaCalculator.cc <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="shell"><span class="nt" style="color: #000080;">-lz</span> <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-o</span> diamond</span></pre>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#ba308c53c268704c3008f5e2e6e8129f9f6bf3fe"><strong>src/ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[0.9.26]</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- Fixed a bug that could cause undefined behaviour when using a database file of format version < 2.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">- Fixed a compiler error when compiled as generic C++.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">- Program will no longer terminate with an error if unlink system call fails.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">- Added option `--tantan-minMaskProb` to set minimum repeat probability for tantan masking and changed the default value to 0.9.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">- Added option `--tantan-maxRepeatOffset` to set maximum tandem repeat period to consider and changed the default value to 15.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">- Added option `--tantan-ungapped` to use tantan in ungapped mode and changed the default to gapped mode.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">- Changed score matrix lambda calculation for tantan masking.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">- Reference masking is recomputed during alignment runs.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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1
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">[0.9.25]</span>
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2
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">- Added support for the `sscinames` output field to print subject scientific names to the tabular output format.</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">- Fixed a compiler error for GCC 8.2.</span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#c8d7bd122d50035cfb1627dbd9659f00b8137ded"><strong>src/align/banded_swipe_pipeline.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="165" 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">@@ -165,7 +165,6 @@ void build_ranking_worker(PtrVector<::Target>::iterator begin, PtrVector<::Targe</td>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Pipeline</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">Statistics</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stat</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="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//cout << "Query=" << query_ids::get()[this->query_id].c_str() << endl;</span></span>
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169
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">task_timer</span> <span class="n" style="color: #333;">timer</span><span class="p">(</span><span class="s" style="color: #d14;">"Init banded swipe pipeline"</span><span class="p">,</span> <span class="n" style="color: #333;">target_parallel</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">UINT_MAX</span><span class="p">);</span></span>
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170
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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;">Config</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">set_option</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">padding</span><span class="p">,</span> <span class="mi" style="color: #099;">32</span><span class="p">);</span></span>
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171
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n_targets</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#76d5a97c09cca591280144de40f9c04a5ec57ef7"><strong>src/basic/basic.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">@@ -24,7 +24,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.</td>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "sequence.h"</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "masking.h"</span></span>
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26
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"></span>
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27
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<pre style="margin: 0;">-<span id="LC27" 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;">"0.9.2<span class="idiff left right">5</span>"</span><span class="p">;</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" 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;">"0.9.2<span class="idiff left right">6</span>"</span><span class="p">;</span></span>
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28
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<pre style="margin: 0;"> <span id="LC28" 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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29
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29
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<pre style="margin: 0;"> <span id="LC29" 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;">id_delimiters</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" </span><span class="se" style="color: #d14;">\a\b\f\n\r\t\v\1</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#fe8c534c15ea9cf93547993244c3ab903c4895ff"><strong>src/basic/config.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -197,7 +197,10 @@ Config::Config(int argc, const char **argv)</td>
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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="p">(</span><span class="s" style="color: #d14;">"dbsize"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"effective database size (in letters)"</span><span class="p">,</span> <span class="n" style="color: #333;">db_size</span><span class="p">)</span></span>
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198
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"no-auto-append"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"disable auto appending of DAA and DMND file extensions"</span><span class="p">,</span> <span class="n" style="color: #333;">no_auto_append</span><span class="p">)</span></span>
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199
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"xml-blord-format"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"Use gnl|BL_ORD_ID| style format in XML output"</span><span class="p">,</span> <span class="n" style="color: #333;">xml_blord_format</span><span class="p">)</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"stop-match-score"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"Set the match score of stop codons against each other."</span><span class="p">,</span> <span class="n" style="color: #333;">stop_match_score</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"stop-match-score"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"Set the match score of stop codons against each other."</span><span class="p">,</span> <span class="n" style="color: #333;">stop_match_score</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"tantan-minMaskProb"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"minimum repeat probability for masking (0.9)"</span><span class="p">,</span> <span class="n" style="color: #333;">tantan_minMaskProb</span><span class="p">,</span> <span class="mf" style="color: #099;">0.9</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"tantan-maxRepeatOffset"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"maximum tandem repeat period to consider (50)"</span><span class="p">,</span> <span class="n" style="color: #333;">tantan_maxRepeatOffset</span><span class="p">,</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"tantan-ungapped"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"use tantan masking in ungapped mode"</span><span class="p">,</span> <span class="n" style="color: #333;">tantan_ungapped</span><span class="p">);</span></span>
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201
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"></span>
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202
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<td class="diff-line-num new_line" data-linenumber="205" 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">
205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">Options_group</span> <span class="n" style="color: #333;">view_options</span><span class="p">(</span><span class="s" style="color: #d14;">"View options"</span><span class="p">);</span></span>
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203
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">view_options</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="274" 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="277" 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">@@ -274,8 +277,6 @@ Config::Config(int argc, const char **argv)</td>
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274
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<td class="diff-line-num new_line" data-linenumber="277" 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">
277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"query-parallel-limit"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">query_parallel_limit</span><span class="p">,</span> <span class="mi" style="color: #099;">1000000u</span><span class="p">)</span></span>
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275
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<td class="diff-line-num new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"hard-masked"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">hardmasked</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
276
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<td class="diff-line-num new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"cbs-window"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">cbs_window</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
277
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<td class="diff-line-num new_line old" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"tantan-r"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">tantan_r</span><span class="p">,</span> <span class="mf" style="color: #099;">0.005</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
278
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<td class="diff-line-num new_line old" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"tantan-s"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">tantan_s</span><span class="p">,</span> <span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
279
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<td class="diff-line-num new_line" data-linenumber="280" 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">
280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"no-unlink"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">no_unlink</span><span class="p">)</span></span>
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280
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<td class="diff-line-num new_line" data-linenumber="281" 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">
281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"no-dict"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">no_dict</span><span class="p">);</span></span>
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281
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"> </span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#79a175a8b141cc4f06683108fcd39b79a555f1cd"><strong>src/basic/config.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="175" 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="175" 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">@@ -175,10 +175,12 @@ struct Config</td>
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175
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<td class="diff-line-num new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">hardmasked</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="176" 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">
176
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cbs_window</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="177" 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">
177
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<td class="diff-line-num new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tantan_r</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<td class="diff-line-num new_line old" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tantan_<span class="idiff left right">s</span></span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tantan_<span class="idiff left right">minMaskProb</span></span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="179" 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">
179
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<td class="diff-line-num new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">no_unlink</span><span class="p">;</span></span>
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180
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">no_dict</span><span class="p">;</span></span>
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181
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">stop_match_score</span><span class="p">;</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tantan_maxRepeatOffset</span><span class="p">;</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">tantan_ungapped</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="c"> <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span></span>
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="c"> <span class="n" style="color: #333;">makedb</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;">blastp</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;">blastx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">view</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="n" style="color: #333;">getseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="n" style="color: #333;">random_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="n" style="color: #333;">compare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="n" style="color: #333;">sort</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">roc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">11</span><span class="p">,</span> <span class="n" style="color: #333;">db_stat</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="n" style="color: #333;">model_sim</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">13</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#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">@@ -23,7 +23,7 @@ struct Const</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC25" 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="LC26" 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;">12<span class="idiff left right">6</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC26" 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;">12<span class="idiff left right">7</span></span><span class="p">,</span></span>
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27
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<pre style="margin: 0;"> <span id="LC27" 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;">10</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;">seedp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">seedp_bits</span><span class="p">,</span></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"> <span class="n" style="color: #333;">max_seed_weight</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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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#992408bab41b605763e629e7a719178aef609bae"><strong>src/basic/masking.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">@@ -17,8 +17,10 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">****/</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "masking.h"</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../lib/tantan/tantan.hh"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../lib/tantan/LambdaCalculator.hh"</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" 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">@@ -27,12 +29,21 @@ const uint8_t Masking::bit_mask = 128;</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="n" style="color: #333;">Masking</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Masking</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score_matrix</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">score_matrix</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</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;">lambda</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">// 0.324032</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;">unsigned</span> <span class="n" style="color: #333;">n</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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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">int_matrix</span><span class="p">[</span><span class="mi" style="color: #099;">20</span><span class="p">][</span><span class="mi" style="color: #099;">20</span><span class="p">],</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">int_matrix_ptr</span><span class="p">[</span><span class="mi" style="color: #099;">20</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">int_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">int_matrix</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">int_matrix_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC35" 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;">20</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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<pre style="margin: 0;">+<span id="LC36" 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;">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="mi" style="color: #099;">20</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">int_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score_matrix</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span><span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">cbrc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LambdaCalculator</span> <span class="n" style="color: #333;">lc</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">lc</span><span class="p">.</span><span class="n" style="color: #333;">calculate</span><span class="p">(</span><span class="n" style="color: #333;">int_matrix_ptr</span><span class="p">,</span> <span class="mi" style="color: #099;">20</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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lc</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">// 0.324032</span></span>
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<pre style="margin: 0;"> <span id="LC42" 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;">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;">size</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">mask_table_x_</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;">value_traits</span><span class="p">.</span><span class="n" style="color: #333;">mask_char</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">mask_table_bit_</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</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;">bit_mask</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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;">size</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left">value_traits</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">alphabet_size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">value_traits</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">alphabet_size</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left">n</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">n</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">likelihoodRatioMatrix_</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">lambda</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;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">likelihoodRatioMatrix_</span><span class="p">,</span> <span class="n" style="color: #333;">likelihoodRatioMatrix_</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">probMatrixPointers_</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">@@ -44,22 +55,22 @@ Masking::Masking(const Score_matrix &score_matrix)</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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Masking</span><span class="o" style="font-weight: 600;">::</span><span class="k" style="font-weight: 600;">operator</span><span class="p">()(</span><span class="n" style="color: #333;">Letter</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">len</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="LC57" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">maskSequences</span><span class="p">((</span><span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">),</span> <span class="mi" style="color: #099;"><span class="idiff left right">50</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">maskSequences</span><span class="p">((</span><span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">),</span> <span class="n" style="color: #333;"><span class="idiff left">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">tantan_maxRepeatOffset</span></span><span class="p">,</span></span>
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48
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">const_double_ptr</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">probMatrixPointers_</span><span class="p">,</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">tantan_r</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0.05</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="mf" style="color: #099;"><span class="idiff left right">0.005</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0.05</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="mf" style="color: #099;">0.9</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">tantan_<span class="idiff left right">s</span></span><span class="p">,</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">mask_table_x_</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tantan_ungapped</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">firstGapProb_</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tantan_ungapped</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">otherGapProb_</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">tantan_<span class="idiff left right">minMaskProb</span></span><span class="p">,</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">mask_table_x_</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Masking</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mask_bit</span><span class="p">(</span><span class="n" style="color: #333;">Letter</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">len</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="LC67" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">maskSequences</span><span class="p">((</span><span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">),</span> <span class="mi" style="color: #099;"><span class="idiff left right">50</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">maskSequences</span><span class="p">((</span><span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">),</span> <span class="n" style="color: #333;"><span class="idiff left">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">tantan_maxRepeatOffset</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">const_double_ptr</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">probMatrixPointers_</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">tantan_r</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0.05</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="mf" style="color: #099;"><span class="idiff left right">0.005</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0.05</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="mf" style="color: #099;">0.9</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">tantan_<span class="idiff left right">s</span></span><span class="p">,</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">mask_table_bit_</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tantan_ungapped</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">firstGapProb_</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tantan_ungapped</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">otherGapProb_</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">tantan_<span class="idiff left right">minMaskProb</span></span><span class="p">,</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">mask_table_bit_</span><span class="p">);</span></span>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"><span class="p">}</span></span>
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"></span>
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Masking</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bit_to_hard_mask</span><span class="p">(</span><span class="n" style="color: #333;">Letter</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="99" 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">@@ -88,7 +99,7 @@ void mask_worker(Atomic<size_t> *next, Sequence_set *seqs, const Masking *maskin</td>
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88
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">masking</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mask_bit</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ptr</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">seqs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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89
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"><span class="p">}</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">void</span></span> <span class="nf" style="color: #900; font-weight: 600;">mask_seqs</span><span class="p">(</span><span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Masking</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">masking</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hard_mask</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="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">size_t</span></span> <span class="nf" style="color: #900; font-weight: 600;">mask_seqs</span><span class="p">(</span><span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Masking</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">masking</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hard_mask</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="p">{</span></span>
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">threads</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">Atomic</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">next</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="96" 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="107" 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">@@ -96,4 +107,8 @@ void mask_seqs(Sequence_set &seqs, const Masking &masking, bool hard_mask)</td>
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96
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">mask_worker</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">next</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">masking</span><span class="p">,</span> <span class="n" style="color: #333;">hard_mask</span><span class="p">);</span></span>
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97
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">threads</span><span class="p">)</span></span>
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98
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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;">t</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="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;">0</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="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;">seqs</span><span class="p">.</span><span class="n" style="color: #333;">get_length</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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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">data</span><span class="p">(),</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">value_traits</span><span class="p">.</span><span class="n" style="color: #333;">mask_char</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#e64142605ff8612313a434ebbb47a669146a4d86"><strong>src/basic/masking.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">@@ -41,4 +41,4 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">mask_table_x_</span><span class="p">[</span><span class="n" style="color: #333;">size</span><span class="p">],</span> <span class="n" style="color: #333;">mask_table_bit_</span><span class="p">[</span><span class="n" style="color: #333;">size</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">mask_seqs</span><span class="p">(</span><span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Masking</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">masking</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">hard_mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span></pre>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="nf" style="color: #900; font-weight: 600;">mask_seqs</span><span class="p">(</span><span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Masking</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">masking</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">hard_mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#bb140dcc3945bad51e678d633d41915c87344b2f"><strong>src/data/ref_dictionary.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">@@ -99,7 +99,7 @@ void ReferenceDictionary::build_lazy_dict(DatabaseFile &db_file)</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">db_file</span><span class="p">.</span><span class="n" style="color: #333;">rewind</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">block_to_database_id</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;">db_file</span><span class="p">.</span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">block_to_database_id</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;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">false</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_seqs</span><span class="o" style="font-weight: 600;">::</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;">ref_ids</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filter</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">db_file</span><span class="p">.</span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">block_to_database_id</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;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_seqs</span><span class="o" style="font-weight: 600;">::</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;">ref_ids</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filter</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">dict_to_lazy_dict_id_</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">dict_to_lazy_dict_id_</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">dict_size</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#4c75bd371ff8a5ac8f8c6c03800a0d197a6baf78"><strong>src/data/reference.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">@@ -79,13 +79,13 @@ struct Pos_record</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">DatabaseFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">init</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"><span class="p">{</span></span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">read_header</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">,</span> <span class="n" style="color: #333;">ref_header</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">header2</span><span class="p">;</span></span>
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83
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ref_header</span><span class="p">.</span><span class="n" style="color: #333;">build</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_build_required</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ref_header</span><span class="p">.</span><span class="n" style="color: #333;">db_version</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MIN_DB_VERSION</span><span class="p">)</span></span>
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84
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">(</span><span class="s" style="color: #d14;">"Database was built with an older version of Diamond and is incompatible."</span><span class="p">);</span></span>
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85
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ref_header</span><span class="p">.</span><span class="n" style="color: #333;">db_version</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ReferenceHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">current_db_version</span><span class="p">)</span></span>
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86
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">(</span><span class="s" style="color: #d14;">"Database was built with a newer version of Diamond and is incompatible."</span><span class="p">);</span></span>
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87
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ref_header</span><span class="p">.</span><span class="n" style="color: #333;">sequences</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="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">(</span><span class="s" style="color: #d14;">"Incomplete database file. Database building did not complete successfully."</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">header2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">pos_array_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ref_header</span><span class="p">.</span><span class="n" style="color: #333;">pos_array_offset</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"><span class="p">}</span></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" 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="268" 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">@@ -268,7 +268,7 @@ void DatabaseFile::seek_direct() {</td>
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">ReferenceHeader</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;">ReferenceHeader2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp"></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">DatabaseFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">block_to_database_id</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">max_letters</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">masked</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">dst_seq</span><span class="p">,</span> <span class="n" style="color: #333;">String_set</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">dst_id</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">load_ids</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">filter</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">DatabaseFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">block_to_database_id</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">max_letters</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">dst_seq</span><span class="p">,</span> <span class="n" style="color: #333;">String_set</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">dst_id</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">load_ids</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">filter</span><span class="p">)</span></span>
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272
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"><span class="p">{</span></span>
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273
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"> <span class="n" style="color: #333;">task_timer</span> <span class="n" style="color: #333;">timer</span><span class="p">(</span><span class="s" style="color: #d14;">"Loading reference sequences"</span><span class="p">);</span></span>
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274
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"> <span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="n" style="color: #333;">pos_array_offset</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -318,7 +318,6 @@ bool DatabaseFile::load_seqs(vector<unsigned> &block_to_database_id, size_t max_</td>
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318
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finish_reserve</span><span class="p">();</span></span>
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319
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">load_ids</span><span class="p">)</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_id</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finish_reserve</span><span class="p">();</span></span>
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320
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="n" style="color: #333;">start_offset</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">masked_letters</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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322
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"></span>
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323
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322
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<pre style="margin: 0;"> <span id="LC322" 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;">n</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;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">seqs</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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324
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">filtered_pos</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">])</span> <span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="n" style="color: #333;">filtered_pos</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="329" 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="328" 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">@@ -329,16 +328,12 @@ bool DatabaseFile::load_seqs(vector<unsigned> &block_to_database_id, size_t max_</td>
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329
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"> <span class="n" style="color: #333;">read</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_id</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ptr</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">),</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_id</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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330
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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331
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">seek_forward</span><span class="p">(</span><span class="sc" style="color: #d14;">'\0'</span><span class="p">))</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">(</span><span class="s" style="color: #d14;">"Unexpected end of file."</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC332" 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;">masking</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">masked</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="cpp"> <span class="n" style="color: #333;">Masking</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;">bit_to_hard_mask</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ptr</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">),</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">),</span> <span class="n" style="color: #333;">masked_letters</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;">Masking</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;">remove_bit_mask</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ptr</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">),</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</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="LC331" class="line" lang="cpp"> <span class="n" style="color: #333;">Masking</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;">remove_bit_mask</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ptr</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">),</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">));</span></span>
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336
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">sfilt</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strstr</span><span class="p">((</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">dst_id</span><span class="p">)[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">sfilt</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">())</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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337
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ptr</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">),</span> <span class="n" style="color: #333;">value_traits</span><span class="p">.</span><span class="n" style="color: #333;">mask_char</span><span class="p">,</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">));</span></span>
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338
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp"> <span class="p">}</span></span>
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339
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;">timer</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">();</span></span>
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340
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">print_stats</span><span class="p">();</span></span>
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341
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">log_stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Masked letters = "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">masked_letters</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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342
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"></span>
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343
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">blocked_processing</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqs_processed</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ref_header</span><span class="p">.</span><span class="n" style="color: #333;">sequences</span><span class="p">;</span></span>
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344
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#b4ebfd635f4bc15a73d7a817b3af743fc2daf57a"><strong>src/data/reference.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="80" 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">@@ -80,7 +80,7 @@ struct DatabaseFile : public InputFile</td>
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80
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">DatabaseFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">auto_create_from_fasta</span><span class="p">();</span></span>
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81
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">is_diamond_db</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">file_name</span><span class="p">);</span></span>
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82
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">rewind</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">block_to_database_id</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">max_letters</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">masked</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">dst_seq</span><span class="p">,</span> <span class="n" style="color: #333;">String_set</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">dst_id</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">load_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">block_to_database_id</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">max_letters</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">dst_seq</span><span class="p">,</span> <span class="n" style="color: #333;">String_set</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">dst_id</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">load_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">get_seq</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">read_seq</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">has_taxon_id_lists</span><span class="p">();</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#8366fdef1b3e7c06b4325bf704ef6a9a25477168"><strong>src/data/seed_array.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">@@ -93,7 +93,7 @@ struct BuildCallback</td>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">_filter</span><span class="o" style="font-weight: 600;">></span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"><span class="n" style="color: #333;">SeedArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SeedArray</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">shape</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">shape_histogram</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hst</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SeedPartitionRange</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">range</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seq_partition</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_filter</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">filter</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"><span class="n" style="color: #333;">SeedArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SeedArray</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">shape</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">shape_histogram</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hst</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SeedPartitionRange</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">range</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">seq_partition</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_filter</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">filter</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"><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;">task_timer</span> <span class="n" style="color: #333;">timer</span><span class="p">(</span><span class="s" style="color: #d14;">"Allocating memory for seed array"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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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;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">range</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">range</span><span class="p">.</span><span class="n" style="color: #333;">end</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">@@ -108,6 +108,6 @@ SeedArray::SeedArray(const Sequence_set &seqs, size_t shape, const shape_histogr</td>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">seqs</span><span class="p">.</span><span class="n" style="color: #333;">enum_seeds</span><span class="p">(</span><span class="n" style="color: #333;">cb</span><span class="p">,</span> <span class="n" style="color: #333;">seq_partition</span><span class="p">,</span> <span class="n" style="color: #333;">shape</span><span class="p">,</span> <span class="n" style="color: #333;">shape</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;">filter</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="n" style="color: #333;">SeedArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SeedArray</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">shape_histogram</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;">SeedPartitionRange</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">No_filter</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="n" style="color: #333;">SeedArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SeedArray</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">shape_histogram</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;">SeedPartitionRange</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">Seed_set</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="n" style="color: #333;">SeedArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SeedArray</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">shape_histogram</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;">SeedPartitionRange</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">Hashed_seed_set</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span></pre>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="n" style="color: #333;">SeedArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SeedArray</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">shape_histogram</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;">SeedPartitionRange</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">No_filter</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="n" style="color: #333;">SeedArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SeedArray</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">shape_histogram</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;">SeedPartitionRange</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">Seed_set</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="n" style="color: #333;">SeedArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SeedArray</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">shape_histogram</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;">SeedPartitionRange</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">Hashed_seed_set</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</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">@@ -45,7 +45,7 @@ struct SeedArray</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="p">}</span> <span class="n" style="color: #333;">PACKED_ATTRIBUTE</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">_filter</span><span class="o" style="font-weight: 600;">></span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">SeedArray</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">shape</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">shape_histogram</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hst</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SeedPartitionRange</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">range</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seq_partition</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_filter</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">filter</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">SeedArray</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence_set</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">shape</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">shape_histogram</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hst</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SeedPartitionRange</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">range</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">seq_partition</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_filter</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">filter</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">Entry</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">begin</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#79ac9d06e448a7f7da92ca7130fc5d7818aaf460"><strong>src/dp/needleman_wunsch.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">@@ -167,7 +167,7 @@ const Fixed_score_buffer<_score>& needleman_wunsch(sequence query, sequence subj</td>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mtx</span><span class="p">.</span><span class="n" style="color: #333;">score_buffer</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Fixed_score_buffer</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">needleman_wunsch</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">subject</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_score</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Local</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Fixed_score_buffer</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">needleman_wunsch</span><span class="o" style="font-weight: 600;"><span class="idiff left"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Local</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">></span></span><span class="p">(</span><span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">subject</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_score</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Local</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">needleman_wunsch</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">subject</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qbegin</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qend</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sbegin</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">send</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">node</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">edge</span><span class="p">,</span> <span class="n" style="color: #333;">Diag_graph</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">diags</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">log</span><span class="p">)</span></span>
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"><span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#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">@@ -233,6 +233,26 @@ void banded_3frame_swipe(const TranslatedSequence &query, Strand strand, vector<</td>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">_sv</span><span class="o" style="font-weight: 600;">></span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">banded_3frame_swipe_targets</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">begin</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">end</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">score_only</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TranslatedSequence</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">query</span><span class="p">,</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">Strand</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">DpStat</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stat</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">parallel</span><span class="p">,</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">overflow_only</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"><span class="p">{</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">begin</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;">end</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="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">overflow_only</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overflow</span><span class="p">)</span> <span class="p">{</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score_only</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">disable_traceback</span><span class="p">)</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe</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;">ScoreOnly</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">i</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">difference_type</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 class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="n" style="color: #333;">parallel</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe</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;">Traceback</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">i</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">difference_type</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 class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="n" style="color: #333;">parallel</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">banded_3frame_swipe_worker</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">begin</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">end</span><span class="p">,</span></span>
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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;">Atomic</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">next</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">@@ -242,15 +262,12 @@ void banded_3frame_swipe_worker(vector<DpTarget>::iterator begin,</td>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"> <span class="n" style="color: #333;">DpStat</span> <span class="n" style="color: #333;">stat</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">begin</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">post_add</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">swipe_chunk_size</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC246" 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;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">begin</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">swipe_chunk_size</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">begin</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pos</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;">e</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;">8</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score_only</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">disable_traceback</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">score_vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">></span><span class="p">,</span> <span class="n" style="color: #333;">ScoreOnly</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;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">min</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;">8</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">),</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">score_vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">></span><span class="p">,</span> <span class="n" style="color: #333;">Traceback</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;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">min</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;">8</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">),</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">begin</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">post_add</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">swipe_chunk_size</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __SSE2__</span></span>
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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe_targets</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">score_vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">>></span><span class="p">(</span><span class="n" style="color: #333;">begin</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">begin</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">swipe_chunk_size</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">),</span> <span class="n" style="color: #333;">score_only</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe_targets</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">begin</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">begin</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">swipe_chunk_size</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">),</span> <span class="n" style="color: #333;">score_only</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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254
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"><span class="p">}</span></span>
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255
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"></span>
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256
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">banded_3frame_swipe</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TranslatedSequence</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">Strand</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">target_begin</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">target_end</span><span class="p">,</span> <span class="n" style="color: #333;">DpStat</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">score_only</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">parallel</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="278" 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">@@ -278,26 +295,11 @@ void banded_3frame_swipe(const TranslatedSequence &query, Strand strand, vector<</td>
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278
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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279
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp"> <span class="p">}</span></span>
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280
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="p">}</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target_begin</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;">target_end</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;">8</span><span class="p">)</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score_only</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">disable_traceback</span><span class="p">)</span></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">score_vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">></span><span class="p">,</span> <span class="n" style="color: #333;">ScoreOnly</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">i</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">difference_type</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">),</span> <span class="n" style="color: #333;">target_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">score_vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">></span><span class="p">,</span> <span class="n" style="color: #333;">Traceback</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">i</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">difference_type</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">),</span> <span class="n" style="color: #333;">target_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="cpp"> <span class="p">}</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe_targets</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">score_vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">>></span><span class="p">(</span><span class="n" style="color: #333;">target_begin</span><span class="p">,</span> <span class="n" style="color: #333;">target_end</span><span class="p">,</span> <span class="n" style="color: #333;">score_only</span><span class="p">,</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target_begin</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;">target_end</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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<pre style="margin: 0;">-<span id="LC290" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overflow</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score_only</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">disable_traceback</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">,</span> <span class="n" style="color: #333;">ScoreOnly</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">i</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;">1</span><span class="p">,</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">,</span> <span class="n" style="color: #333;">Traceback</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">i</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;">1</span><span class="p">,</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe_targets</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">target_begin</span><span class="p">,</span> <span class="n" style="color: #333;">target_end</span><span class="p">,</span> <span class="n" style="color: #333;">score_only</span><span class="p">,</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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296
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<pre style="margin: 0;"> <span id="LC302" 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="LC297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target_begin</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;">target_end</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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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score_only</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">disable_traceback</span><span class="p">)</span></span>
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299
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">,</span> <span class="n" style="color: #333;">ScoreOnly</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">i</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;">1</span><span class="p">,</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">,</span> <span class="n" style="color: #333;">Traceback</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">i</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;">1</span><span class="p">,</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">banded_3frame_swipe_targets</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">target_begin</span><span class="p">,</span> <span class="n" style="color: #333;">target_end</span><span class="p">,</span> <span class="n" style="color: #333;">score_only</span><span class="p">,</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC304" 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="LC305" class="line" lang="cpp"><span class="p">}</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/30dedeaf53a7c61254b0a923de683bb50b14fc30#61f8e8d714778e5355aa05d2be26c9fef3c4f128"><strong>src/lib/tantan/LambdaCalculator.cc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2015 Yutaro Konta</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "LambdaCalculator.hh"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cassert></span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstdio> // sprintf</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstdlib></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cfloat></span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cmath></span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#include <iostream></span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">roundToFewDigits</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// This rounding fixes some inaccuracies, e.g. for DNA with a simple</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// match/mismatch matrix it's likely to make all the probabilities</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// exactly 0.25, as they should be.</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">32</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="s" style="color: #d14;">"%g"</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="LC20" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">atof</span><span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"></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;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="nf" style="color: #900; font-weight: 600;">makematrix</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">val</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="p">[</span><span class="n" style="color: #333;">m</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;">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;">m</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">mat</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="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</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="LC29" 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;">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;">n</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">mat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <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;">return</span> <span class="n" style="color: #333;">mat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><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="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">deletematrix</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC37" 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;">m</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"><span class="p">}</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">summatrix</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"><span class="p">{</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">s</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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45
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<pre style="margin: 0;">+<span id="LC45" 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;">m</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" 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;">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;">n</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="p">}</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">max_index</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"><span class="p">{</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">DBL_MAX</span><span class="p">;</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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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;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">i</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;">n</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</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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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">j</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;">max</span><span class="p">)</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="p">{</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">maxindex</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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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="p">}</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="p">}</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">maxindex</span><span class="p">;</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"><span class="p">}</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" 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="nf" style="color: #900; font-weight: 600;">swap_matrix</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">a</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"><span class="p">{</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">a</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;">a</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">a</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;">v</span><span class="p">;</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"><span class="p">}</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" 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="nf" style="color: #900; font-weight: 600;">swap_vector</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">a</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"><span class="p">{</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">a</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;">a</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">a</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;">v</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">lu_pivoting</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"><span class="p">{</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">v</span><span class="p">;</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"></span>
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85
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<pre style="margin: 0;">+<span id="LC85" 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;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">idx</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;">i</span><span class="p">;</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"></span>
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88
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<pre style="margin: 0;">+<span id="LC88" 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;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="p">{</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_index</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">v</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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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">v</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="mf" style="color: #099;">1e-10</span><span class="p">)</span></span>
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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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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// singular matrix!</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="p">}</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">swap_matrix</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">);</span></span>
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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;">swap_vector</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">);</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"></span>
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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;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</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="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span 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;">j</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</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="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;">a</span><span class="p">[</span><span class="n" style="color: #333;">j</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;">a</span><span class="p">[</span><span class="n" style="color: #333;">j</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;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">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;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">j</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;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="p">}</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="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="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"><span class="p">}</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" 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="nf" style="color: #900; font-weight: 600;">solvep</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"><span class="p">{</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">];</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"></span>
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115
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<pre style="margin: 0;">+<span id="LC115" 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;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="p">{</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">y</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;">b</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span 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;">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;">i</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">y</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;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="p">}</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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;">n</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;">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="p">)</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="p">{</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">x</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;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="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;">j</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">x</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;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">j</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="cpp"> <span class="n" style="color: #333;">x</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;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// needed because a[i][i] is inverted</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="p">}</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"><span class="p">}</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">transpose</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"><span class="p">{</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">v</span><span class="p">;</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" 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;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="p">{</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" 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;">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;">i</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="p">{</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">j</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;">v</span><span class="p">;</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="p">}</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="p">}</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"><span class="p">}</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">invert</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"><span class="p">{</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">];</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">makematrix</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">lu_pivoting</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">))</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"></span>
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155
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<pre style="margin: 0;">+<span id="LC155" 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;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">e</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">[</span><span class="n" style="color: #333;">i</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="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// transposed</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">idx</span><span class="p">;</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"></span>
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160
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<pre style="margin: 0;">+<span id="LC160" 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;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">solvep</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">inv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">e</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">deletematrix</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">transpose</span><span class="p">(</span><span class="n" style="color: #333;">inv</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// transpose inv to make the inverted matrix of a</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"><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>
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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;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">calculate_inv_sum</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tau</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">inv_sum</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="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">makematrix</span><span class="p">(</span><span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">makematrix</span><span class="p">(</span><span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" 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;">alpha_size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" 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;">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;">alpha_size</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">tau</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">invert</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">))</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inv_sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">summatrix</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">);</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">deletematrix</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">);</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">deletematrix</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">);</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"><span class="p">}</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span><span class="p">{</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">LambdaCalculator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setBad</span><span class="p">(){</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">lambda_</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"> <span class="n" style="color: #333;">letterProbs1_</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">letterProbs2_</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><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 class="p">}</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">LambdaCalculator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">find_ub</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ub</span><span class="p">)</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"><span class="p">{</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">r_max_min</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DBL_MAX</span><span class="p">;</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">c_max_min</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DBL_MAX</span><span class="p">;</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">r_max</span><span class="p">;</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">c_max</span><span class="p">;</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">r_min</span><span class="p">;</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">c_min</span><span class="p">;</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l_r</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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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l_c</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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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"></span>
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208
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<pre style="margin: 0;">+<span id="LC208" 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;">alpha_size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="p">{</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">r_max</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">DBL_MAX</span><span class="p">;</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">r_min</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DBL_MAX</span><span class="p">;</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" 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;">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;">alpha_size</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="p">{</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">r_max</span><span class="p">)</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">r_max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">r_min</span><span class="p">)</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">r_min</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="p">}</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r_max</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r_min</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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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">l_r</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r_max</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r_min</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="LC223" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r_max</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">r_max_min</span><span class="p">)</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">r_max_min</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r_max</span><span class="p">;</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="p">}</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"></span>
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228
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<pre style="margin: 0;">+<span id="LC228" 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;">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;">alpha_size</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="p">{</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="n" style="color: #333;">c_max</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">DBL_MAX</span><span class="p">;</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">c_min</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DBL_MAX</span><span class="p">;</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" 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;">alpha_size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="p">{</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">c_max</span><span class="p">)</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">c_max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">c_min</span><span class="p">)</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="n" style="color: #333;">c_min</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="p">}</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c_max</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">c_min</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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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">l_c</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c_max</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">c_min</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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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><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;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c_max</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">c_max_min</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">c_max_min</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c_max</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="p">}</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l_r</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// the multiplication by 1.1 is sometimes necessary, presumably to</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// prevent the upper bound from being too tight:</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r_max_min</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">c_max_min</span><span class="p">)</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ub</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">alpha_size</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">l_r</span><span class="p">))</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">r_max_min</span><span class="p">;</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ub</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">alpha_size</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">l_c</span><span class="p">))</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">c_max_min</span><span class="p">;</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"><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>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">LambdaCalculator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">binary_search</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lb</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ub</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">letprob1</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">letprob2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxiter</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="p">{</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">l</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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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">r</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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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">l_sum</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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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">r_sum</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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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">iter</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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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxiter</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">l_sum</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r_sum</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">l_sum</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r_sum</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1.0</span><span class="p">)))</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="p">{</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">ub</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lb</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="n" style="color: #333;">RAND_MAX</span><span class="p">;</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">ub</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lb</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="n" style="color: #333;">RAND_MAX</span><span class="p">;</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">calculate_inv_sum</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">l_sum</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">calculate_inv_sum</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">r_sum</span><span class="p">))</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="p">{</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="n" style="color: #333;">l</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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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="p">}</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="p">}</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">maxiter</span><span class="p">)</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">l_sum</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r_sum</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">r</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mf" style="color: #099;">2.0</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">r</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mf" style="color: #099;">2.0</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">r</span><span class="p">)</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="p">{</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mf" style="color: #099;">2.0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mid_sum</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">calculate_inv_sum</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mid_sum</span><span class="p">))</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">mid_sum</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">DBL_MAX</span><span class="p">)</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">l_sum</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mid_sum</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">l_sum</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mid_sum</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">))</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="p">{</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid</span><span class="p">;</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">r_sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid_sum</span><span class="p">;</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="p">}</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">r_sum</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mid_sum</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">r_sum</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mid_sum</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">))</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="p">{</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid</span><span class="p">;</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">l_sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid_sum</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="p">}</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"> <span class="p">}</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">l_sum</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">r_sum</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1.0</span><span class="p">))</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_lambda</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="n" style="color: #333;">letprob1</span><span class="p">,</span> <span class="n" style="color: #333;">letprob2</span><span class="p">))</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"> <span class="p">{</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lambda</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</span><span class="p">;</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="p">}</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="p">}</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_lambda</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="n" style="color: #333;">letprob1</span><span class="p">,</span> <span class="n" style="color: #333;">letprob2</span><span class="p">))</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="p">{</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lambda</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="p">}</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"><span class="p">}</span></span>
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327
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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;">double</span> <span class="n" style="color: #333;">LambdaCalculator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">calculate_lambda</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">letprob1</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">letprob2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxiter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_boundary_search_iter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lb_ratio</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ub</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">find_ub</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ub</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ub</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lb_ratio</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">iter</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="LC338" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxiter</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">binary_search</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="n" style="color: #333;">lb</span><span class="p">,</span> <span class="n" style="color: #333;">ub</span><span class="p">,</span> <span class="n" style="color: #333;">letprob1</span><span class="p">,</span> <span class="n" style="color: #333;">letprob2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="n" style="color: #333;">max_boundary_search_iter</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lambda</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">LambdaCalculator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">check_lambda</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">letprob1</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">letprob2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"><span class="p">{</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">makematrix</span><span class="p">(</span><span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">makematrix</span><span class="p">(</span><span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"></span>
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354
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<pre style="margin: 0;">+<span id="LC354" 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;">alpha_size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" 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;">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;">alpha_size</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">lambda</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="n" style="color: #333;">invert</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">);</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"></span>
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360
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<pre style="margin: 0;">+<span id="LC360" 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;">alpha_size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="p">{</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" 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;">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;">alpha_size</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">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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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="p">{</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="n" style="color: #333;">letprob2</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"> <span class="p">}</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="n" style="color: #333;">letprob2</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">roundToFewDigits</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">));</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <span class="p">}</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"></span>
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373
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<pre style="margin: 0;">+<span id="LC373" 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;">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;">alpha_size</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="p">{</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">q</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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<td class="diff-line-num new new_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
376
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<pre style="margin: 0;">+<span id="LC376" 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;">alpha_size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">q</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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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="p">{</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="n" style="color: #333;">letprob2</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="n" style="color: #333;">letprob1</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"> <span class="p">}</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"> <span class="n" style="color: #333;">letprob1</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">roundToFewDigits</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">));</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="p">}</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"> <span class="n" style="color: #333;">deletematrix</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">);</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"> <span class="n" style="color: #333;">deletematrix</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">);</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"><span class="p">}</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">LambdaCalculator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">calculate</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_int_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alphSize</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">alphSize</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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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">setBad</span><span class="p">();</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxiter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000</span><span class="p">;</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_boundary_search_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lb_ratio</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1e-6</span><span class="p">;</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">makematrix</span><span class="p">(</span><span class="n" style="color: #333;">alphSize</span><span class="p">,</span> <span class="n" style="color: #333;">alphSize</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="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;">alphSize</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" 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;">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;">alphSize</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">mat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="n" style="color: #333;">lambda_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calculate_lambda</span><span class="p">(</span><span class="n" style="color: #333;">mat</span><span class="p">,</span> <span class="n" style="color: #333;">alphSize</span><span class="p">,</span> <span class="n" style="color: #333;">letterProbs1_</span><span class="p">,</span> <span class="n" style="color: #333;">letterProbs2_</span><span class="p">,</span> <span class="n" style="color: #333;">maxiter</span><span class="p">,</span> <span class="n" style="color: #333;">max_boundary_search_iter</span><span class="p">,</span> <span class="n" style="color: #333;">lb_ratio</span><span class="p">);</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="n" style="color: #333;">deletematrix</span><span class="p">(</span><span class="n" style="color: #333;">mat</span><span class="p">,</span> <span class="n" style="color: #333;">alphSize</span><span class="p">);</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"><span class="p">}</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#a0592a74c753eee83c242399a07f04bbb888f2f1"><strong>src/lib/tantan/LambdaCalculator.hh</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2008 Michiaki Hamada</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Modified 2015 Yutaro Konta</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This class calculates the scale factor (lambda), and the letter</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// probabilities, that are implicit in a scoring matrix. The</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// calculation might fail for various reasons, putting it into a</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// "bad/undefined" state.</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// If the score matrix is symmetric, then the two sets of letter</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// probabilities should be identical. With this code, they might</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// differ minutely from exact identity.</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef LAMBDA_CALCULATOR_HH</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define LAMBDA_CALCULATOR_HH</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">const_int_ptr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">LambdaCalculator</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"> <span class="nl">public:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="n" style="color: #333;">LambdaCalculator</span><span class="p">()</span> <span class="p">{</span> <span class="n" style="color: #333;">setBad</span><span class="p">();</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="LC26" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">calculate</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_int_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alphSize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Put us in the bad/undefined state.</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setBad</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Are we in the bad/undefined state?</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isBad</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">lambda_</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// The scale factor. In the bad/undefined state, it is negative.</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lambda_</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// The probabilities of letters corresponding to matrix rows (1st index).</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// In the bad/undefined state, it is a null pointer.</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">letterProbs1</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">isBad</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">letterProbs1_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];}</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// The probabilities of letters corresponding to matrix columns (2nd index).</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// In the bad/undefined state, it is a null pointer.</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">letterProbs2</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">isBad</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">letterProbs2_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];}</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="nl">private:</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">letterProbs1_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">letterProbs2_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">find_ub</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ub</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">binary_search</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alpha_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lb</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ub</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">letprob1</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">letprob2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxiter</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">calculate_lambda</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alpha_size</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">letprob1</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">letprob2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxiter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_boundary_search_iter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lb_ratio</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">check_lambda</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alpha_size</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">letprob1</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">letprob2</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"><span class="p">};</span></span>
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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="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// end namespace</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;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#7d9733b309ffca9c00e603bbc75bdef36b121081"><strong>src/run/cluster.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">@@ -121,7 +121,7 @@ void run() {</td>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">String_set</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rep_ids</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">rep_database_id</span><span class="p">,</span> <span class="n" style="color: #333;">rep_block_id</span><span class="p">(</span><span class="n" style="color: #333;">seq_count</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rewind</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">rep_database_id</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="mf" style="color: #099;">1e11</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">true</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rep_seqs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rep_ids</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rep2</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">rep_database_id</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="mf" style="color: #099;">1e11</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rep_seqs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rep_ids</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rep2</span><span class="p">);</span></span>
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125
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125
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<pre style="margin: 0;"> <span id="LC125" 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;">rep_database_id</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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126
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">rep_block_id</span><span class="p">[</span><span class="n" style="color: #333;">rep_database_id</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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127
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#aa612a337fc66ae885c76e4eb2a819dfd69117f8"><strong>src/run/double_indexed.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">@@ -129,7 +129,16 @@ void run_ref_chunk(DatabaseFile &db_file,</td>
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">block_to_database_id</span><span class="p">)</span></span>
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130
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"><span class="p">{</span></span>
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131
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">log_stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Current RSS: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">getCurrentRSS</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", Peak RSS: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">getPeakRSS</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">task_timer</span> <span class="n" style="color: #333;">timer</span><span class="p">(</span><span class="s" style="color: #d14;">"Building reference histograms"</span><span class="p">);</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">task_timer</span> <span class="n" style="color: #333;">timer</span><span class="p">;</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">masking</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">timer</span><span class="p">.</span><span class="n" style="color: #333;">go</span><span class="p">(</span><span class="s" style="color: #d14;">"Masking reference"</span><span class="p">);</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <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="n" style="color: #333;">mask_seqs</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_seqs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">,</span> <span class="n" style="color: #333;">Masking</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get</span><span class="p">());</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">timer</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">();</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">log_stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Masked letters: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="p">}</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">timer</span><span class="p">.</span><span class="n" style="color: #333;">go</span><span class="p">(</span><span class="s" style="color: #d14;">"Building reference histograms"</span><span class="p">);</span></span>
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133
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142
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<pre style="margin: 0;"> <span id="LC142" 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;">algo</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">Config</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">query_indexed</span><span class="p">)</span></span>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">ref_hst</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Partitioned_histogram</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_seqs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">query_seeds</span><span class="p">);</span></span>
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135
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">query_seeds_hashed</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -237,7 +246,6 @@ void run_query_chunk(DatabaseFile &db_file,</td>
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237
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"> </span>
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238
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">current_ref_block</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;">db_file</span><span class="p">.</span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">block_to_database_id</span><span class="p">,</span></span>
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239
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">chunk_size</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">1e9</span><span class="p">),</span></span>
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240
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span></span>
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241
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_seqs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">,</span></span>
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242
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_ids</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">,</span></span>
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243
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -308,7 +316,6 @@ void master_thread(DatabaseFile *db_file, Timer &total_timer, Metadata &metadata</td>
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308
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="n" style="color: #333;">db_file</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seek_seq</span><span class="p">(</span><span class="n" style="color: #333;">query_file_offset</span><span class="p">);</span></span>
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309
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">db_file</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">query_block_to_database_id</span><span class="p">,</span></span>
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310
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">chunk_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1e9</span><span class="p">),</span></span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span></span>
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312
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">query_seqs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">,</span></span>
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313
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">query_ids</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">,</span></span>
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314
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span></span>
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<li id="bd735448b4c157cfe3470c9dca2a5f97ef2682db">
<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#bd735448b4c157cfe3470c9dca2a5f97ef2682db"><strong>src/run/tools.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">@@ -46,7 +46,7 @@ void random_seqs()</td>
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46
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"><span class="p">{</span></span>
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47
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">DatabaseFile</span> <span class="n" style="color: #333;">db_file</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">database</span><span class="p">);</span></span>
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48
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">v</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">db_file</span><span class="p">.</span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">v</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;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">true</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_seqs</span><span class="o" style="font-weight: 600;">::</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;">ref_ids</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">db_file</span><span class="p">.</span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">v</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;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_seqs</span><span class="o" style="font-weight: 600;">::</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;">ref_ids</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Sequences = "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ref_seqs</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;">get_length</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC51" 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;">set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <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;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">seq_no</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="89" 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">@@ -89,7 +89,7 @@ void db_stat()</td>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"><span class="p">{</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">DatabaseFile</span> <span class="n" style="color: #333;">db_file</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">database</span><span class="p">);</span></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">v</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">db_file</span><span class="p">.</span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">v</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;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">true</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_seqs</span><span class="o" style="font-weight: 600;">::</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;">ref_ids</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">db_file</span><span class="p">.</span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">v</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;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_seqs</span><span class="o" style="font-weight: 600;">::</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;">ref_ids</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Sequences = "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ref_seqs</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;">get_length</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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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="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">letters</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="116" 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="116" 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">@@ -116,6 +116,7 @@ void run_masker()</td>
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Letter</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FASTA_format</span> <span class="n" style="color: #333;">format</span><span class="p">;</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">letters</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;">seqs</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;">seqs_total</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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119
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">format</span><span class="p">.</span><span class="n" style="color: #333;">get_seq</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">))</span> <span class="p">{</span></span>
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120
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'>'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">(),</span> <span class="n" style="color: #333;">id</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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121
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -128,6 +129,16 @@ void run_masker()</td>
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128
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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129
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cout << endl;*/</span></span>
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130
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sequence</span><span class="p">(</span><span class="n" style="color: #333;">seq2</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">(),</span> <span class="n" style="color: #333;">seq2</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="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;">0</span><span class="p">;</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="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;">seq2</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq2</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;">value_traits</span><span class="p">.</span><span class="n" style="color: #333;">mask_char</span><span class="p">)</span> <span class="p">{</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="p">}</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">letters</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n</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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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seqs</span><span class="p">;</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seqs_total</span><span class="p">;</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"#Sequences: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">seqs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">seqs_total</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", #Letters: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">letters</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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131
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> <span class="p">}</span></span>
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132
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"><span class="p">}</span></span>
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133
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -159,7 +170,7 @@ void test_io()</td>
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159
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"></span>
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160
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">DatabaseFile</span> <span class="n" style="color: #333;">db</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">database</span><span class="p">);</span></span>
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161
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">v</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
162
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<td class="diff-line-num new_line old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">v</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;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">true</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_seqs</span><span class="o" style="font-weight: 600;">::</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;">ref_ids</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">load_seqs</span><span class="p">(</span><span class="n" style="color: #333;">v</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;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_seqs</span><span class="o" style="font-weight: 600;">::</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;">ref_ids</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_</span><span class="p">);</span></span>
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163
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
164
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ref_seqs</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;">raw_len</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ref_ids</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;">raw_len</span><span class="p">();</span></span>
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165
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"MBytes/sec = "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">1e6</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">getElapsedTime</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#d617200d9067f8f78c9396cbc28dc9307c8738cd"><strong>src/util/command_line_parser.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="99" 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">@@ -99,7 +99,7 @@ void Command_line_parser::store(int count, const char ** str, unsigned &command)</td>
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99
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"></span>
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100
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Command_line_parser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">print_help</span><span class="p">()</span></span>
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101
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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="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;">col1_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2<span class="idiff left right">3</span></span><span class="p">;</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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;">col1_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2<span class="idiff left right">5</span></span><span class="p">;</span></span>
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103
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Syntax: diamond COMMAND [OPTIONS]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Commands:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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105
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">commands_</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">commands_</span><span class="p">.</span><span class="n" style="color: #333;">end</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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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#c594ddd20c4c5befe842e4f70eccdc1934b9a261"><strong>src/util/io/file_backed_buffer.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">@@ -27,7 +27,7 @@ struct FileBackedBuffer : public TempFile, public InputFile</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"></span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"> <span class="n" style="color: #333;">FileBackedBuffer</span><span class="p">()</span><span class="o" style="font-weight: 600;">:</span></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"> <span class="n" style="color: #333;">TempFile</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"> <span class="n" style="color: #333;">InputFile</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dynamic_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">Output</span>File</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"> <span class="n" style="color: #333;">InputFile</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dynamic_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">Temp</span>File</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">))</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"></span>
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<li id="1f1991a4cdd1bf9ed0a3e3d9cfa2018c12da9246">
<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#1f1991a4cdd1bf9ed0a3e3d9cfa2018c12da9246"><strong>src/util/io/input_file.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">@@ -29,6 +29,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.</td>
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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 "compressed_stream.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 "input_stream_buffer.h"</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../../basic/config.h"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "temp_file.h"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">is_gzip_stream</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="41" 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">@@ -40,7 +41,8 @@ bool is_gzip_stream(const unsigned char *b)</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"><span class="n" style="color: #333;">InputFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InputFile</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">file_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flags</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">Deserializer</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">InputStreamBuffer</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FileSource</span><span class="p">(</span><span class="n" style="color: #333;">file_name</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;">file_name</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">file_name</span><span class="p">(</span><span class="n" style="color: #333;">file_name</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;">unlinked</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">file_name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>
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46
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="66" 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">@@ -64,9 +66,10 @@ InputFile::InputFile(const string &file_name, int flags) :</td>
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64
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer_</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">InputStreamBuffer</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ZlibSource</span><span class="p">(</span><span class="n" style="color: #333;">buffer_</span><span class="p">));</span></span>
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65
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"><span class="p">}</span></span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"><span class="n" style="color: #333;">InputFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InputFile</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">Output</span>File</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tmp_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flags</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"><span class="n" style="color: #333;">InputFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InputFile</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">Temp</span>File</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tmp_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flags</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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68
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">Deserializer</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">InputStreamBuffer</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FileSource</span><span class="p">(</span><span class="n" style="color: #333;">tmp_file</span><span class="p">.</span><span class="n" style="color: #333;">file_name</span><span class="p">(),</span> <span class="n" style="color: #333;">tmp_file</span><span class="p">.</span><span class="n" style="color: #333;">file</span><span class="p">()))),</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">file_name</span><span class="p">(</span><span class="n" style="color: #333;">tmp_file</span><span class="p">.</span><span class="n" style="color: #333;">file_name</span><span class="p">())</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">file_name</span><span class="p">(</span><span class="n" style="color: #333;">tmp_file</span><span class="p">.</span><span class="n" style="color: #333;">file_name</span><span class="p">()),</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">unlinked</span><span class="p">(</span><span class="n" style="color: #333;">tmp_file</span><span class="p">.</span><span class="n" style="color: #333;">unlinked</span><span class="p">)</span></span>
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70
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_file</span><span class="p">.</span><span class="n" style="color: #333;">rewind</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" 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="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -74,11 +77,6 @@ InputFile::InputFile(OutputFile &tmp_file, int flags) :</td>
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74
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InputFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">close_and_delete</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef WIN32</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">windows</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC79" 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="LC80" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">windows</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC81" 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="LC82" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">windows</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">no_unlink</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">())</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">unlinked</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">())</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: Failed to delete temporary file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">file_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"><span class="p">}</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/30dedeaf53a7c61254b0a923de683bb50b14fc30#2370dc5cead55336c866ff7109bc5eaaa392a9d0"><strong>src/util/io/input_file.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">@@ -29,16 +29,19 @@ using std::vector;</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">TempFile</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">InputFile</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">Deserializer</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">BUFFERED</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">InputFile</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">file_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flags</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="LC38" class="line" lang="c"> <span class="n" style="color: #333;">InputFile</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">Output</span>File</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tmp_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flags</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="LC40" class="line" lang="c"> <span class="n" style="color: #333;">InputFile</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">Temp</span>File</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tmp_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flags</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="LC41" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">close_and_delete</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">file_name</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">unlinked</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"></span>
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<li id="d7cc4906956f41fd1ab5a474f924cefcaca5c537">
<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#d7cc4906956f41fd1ab5a474f924cefcaca5c537"><strong>src/util/io/temp_file.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">@@ -35,6 +35,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "input_file.h"</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">TempFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">n</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="LC41" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">TempFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">hash_key</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">@@ -61,6 +62,7 @@ pair<string, int> TempFile::init()</td>
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<pre style="margin: 0;"> <span id="LC62" 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="LC63" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _MSC_VER</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">unlinked</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">string</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="LC67" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mkstemp</span><span class="p">(</span><span class="n" style="color: #333;">s</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">@@ -68,10 +70,10 @@ pair<string, int> TempFile::init()</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">perror</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"Error opening temporary file "</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">no_unlink</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">unlink</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">s</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">perror</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">throw</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">runtime_error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"Error calling unlink."</span></span><span class="p"><span class="idiff right">);</span></span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"> <span class="p"><span class="idiff left right">}</span></span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">no_unlink</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">unlinked</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left right">else</span></span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">unlinked</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">unlink</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">s</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">);</span></span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">),</span> <span class="n" style="color: #333;">fd</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC78" 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="LC79" class="line" lang="cpp"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/30dedeaf53a7c61254b0a923de683bb50b14fc30#c6904c8405257ade3a64d5717e7b3e7ca86c2f4e"><strong>src/util/io/temp_file.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" 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">@@ -22,22 +22,21 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <utility></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "output_file.h"</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"><span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">TempFile</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">OutputFile</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"> <span class="n" style="color: #333;">TempFile</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">get_temp_dir</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">st<span class="idiff left">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">st</span>ring</span> <span class="n" style="color: #333;">get_temp_dir</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">hash_key</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">unlinked</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="nl">private:</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _MSC_VER</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"> <span class="k" style="font-weight: 600;">st<span class="idiff left">atic</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">init</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">st<span class="idiff left">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">init</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"> <span class="k" style="font-weight: 600;">st<span class="idiff left">atic</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">pair</span></span><span class="o" style="font-weight: 600;"><span class="idiff right"><</span></span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">init</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">st<span class="idiff left">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">pair</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">init</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="p">};</span></span>
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