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<h3>
Nilesh Patra 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/bfb476e4a522c45a09fba4c73f6e0962135133ce">bfb476e4</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-31T15:04:29+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.13</pre>
</li>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="deleted-file">
−
.travis.yml
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<li class="file-stats">
<a href="#ba308c53c268704c3008f5e2e6e8129f9f6bf3fe">
src/ChangeLog
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<li class="file-stats">
<a href="#7540abd0721601ec3b35ecdd671f39ce63cef20f">
src/align/gapped_score.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="#da280a51d91809345347036c4e31920b2c744ab7">
src/basic/const.h
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<li class="file-stats">
<a href="#36c9568495b5e92087ac3999322cf44d3d5cda7d">
src/dp/swipe/banded_3frame_swipe.cpp
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/bfb476e4a522c45a09fba4c73f6e0962135133ce#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">os</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">osx</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - xenial</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">trusty</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">c++</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#addons:</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># apt:</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># packages:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - gdb</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - libclang-common-6.0-dev</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"><span class="na" style="color: #008080;">arch</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">amd64</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">arm64</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ppc64le</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">s390x</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"><span class="na" style="color: #008080;">compiler</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - clang</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span> <span class="s" style="color: #d14;">skip</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir build</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd build</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake -DCMAKE_BUILD_TYPE=Release ..</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - gdb --ex=r -return-child-result -batch -ex bt --args ./diamond test</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - lldb --batch --one-line r --one-line-on-crash bt -- ./diamond test</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./diamond test</span></span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/bfb476e4a522c45a09fba4c73f6e0962135133ce#ba308c53c268704c3008f5e2e6e8129f9f6bf3fe"><strong>src/ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[2.0.13]</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- Fixed a bug that caused invalid bit scores in frameshift alignment mode.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">[2.0.12]</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">- Fixed an error when using HSP filter settings together with a BLAST database.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">- Optimized the performance of alignment traceback.</span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/bfb476e4a522c45a09fba4c73f6e0962135133ce#7540abd0721601ec3b35ecdd671f39ce63cef20f"><strong>src/align/gapped_score.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" style="width: 35px; color: rgba(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">@@ -106,7 +106,7 @@ static void add_dp_targets(const WorkTarget& target, int target_idx, const Seque</td>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">hsp</span><span class="p">[</span><span class="n" style="color: #333;">frame</span><span class="p">].</span><span class="n" style="color: #333;">empty</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">d0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INT_MAX</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INT_MIN</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">j0</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">INT_MAX</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j1</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">INT_MIN</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">bits</span></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="LC109" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">d0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INT_MAX</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INT_MIN</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">score</span></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="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;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Hsp_traits</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hsp</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">hsp</span><span class="p">[</span><span class="n" style="color: #333;">frame</span><span class="p">])</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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">hsp</span><span class="p">.</span><span class="n" style="color: #333;">d_min</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="p">(</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(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="115" style="width: 35px; color: rgba(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">@@ -115,24 +115,23 @@ static void add_dp_targets(const WorkTarget& target, int target_idx, const Seque</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">overlap</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">d0</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;">min_band_overlap</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">overlap</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">b1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">b0</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;">min_band_overlap</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">d0</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;">d0</span><span class="p">,</span> <span class="n" style="color: #333;">b0</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;">d1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">,</span> <span class="n" style="color: #333;">b1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">j0</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;">j0</span><span class="p">,</span> <span class="n" style="color: #333;">hsp</span><span class="p">.</span><span class="n" style="color: #333;">subject_range</span><span class="p">.</span><span class="n" style="color: #333;">begin_</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">j1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">j1</span><span class="p">,</span> <span class="n" style="color: #333;">hsp</span><span class="p">.</span><span class="n" style="color: #333;">subject_range</span><span class="p">.</span><span class="n" style="color: #333;">end_</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">dp_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">)</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">banded_cols</span><span class="p">(</span><span class="n" style="color: #333;">qlen</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">(</span><span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">d0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">bits</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">DP</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BandedSwipe</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bin</span><span class="p">(</span><span class="n" style="color: #333;">hsp_values</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">hsp</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">dp_size</span><span class="p">,</span> <span class="n" style="color: #333;">score_width</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="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">hsp</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d0</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">INT_MAX</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">dp_targets</span><span class="p">[</span><span class="n" style="color: #333;">frame</span><span class="p">][</span><span class="n" style="color: #333;">bits</span><span class="p">].</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">,</span> <span class="n" style="color: #333;">target_idx</span><span class="p">,</span> <span class="n" style="color: #333;">qlen</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d0</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">INT_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">dp_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">)</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">banded_cols</span><span class="p">(</span><span class="n" style="color: #333;">qlen</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">(</span><span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">d0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC123" 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;">bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DP</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BandedSwipe</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bin</span><span class="p">(</span><span class="n" style="color: #333;">hsp_values</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">dp_size</span><span class="p">,</span> <span class="n" style="color: #333;">score_width</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="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">dp_targets</span><span class="p">[</span><span class="n" style="color: #333;">frame</span><span class="p">][</span><span class="n" style="color: #333;">bin</span><span class="p">].</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">,</span> <span class="n" style="color: #333;">target_idx</span><span class="p">,</span> <span class="n" style="color: #333;">qlen</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">d0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">j0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hsp</span><span class="p">.</span><span class="n" style="color: #333;">subject_range</span><span class="p">.</span><span class="n" style="color: #333;">begin_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">j1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hsp</span><span class="p">.</span><span class="n" style="color: #333;">subject_range</span><span class="p">.</span><span class="n" style="color: #333;">end_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">dp_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">)</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">banded_cols</span><span class="p">(</span><span class="n" style="color: #333;">qlen</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">(</span><span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">d0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">DP</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BandedSwipe</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bin</span><span class="p">(</span><span class="n" style="color: #333;">hsp_values</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">hsp</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">dp_size</span><span class="p">,</span> <span class="n" style="color: #333;">score_width</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="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hsp</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">dp_targets</span><span class="p">[</span><span class="n" style="color: #333;">frame</span><span class="p">][</span><span class="n" style="color: #333;">bits</span><span class="p">].</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">,</span> <span class="n" style="color: #333;">target_idx</span><span class="p">,</span> <span class="n" style="color: #333;">qlen</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">dp_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">)</span><span class="n" style="color: #333;">DpTarget</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">banded_cols</span><span class="p">(</span><span class="n" style="color: #333;">qlen</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">(</span><span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">d0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC133" 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;">bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DP</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BandedSwipe</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bin</span><span class="p">(</span><span class="n" style="color: #333;">hsp_values</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">dp_size</span><span class="p">,</span> <span class="n" style="color: #333;">score_width</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="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">dp_targets</span><span class="p">[</span><span class="n" style="color: #333;">frame</span><span class="p">][</span><span class="n" style="color: #333;">bin</span><span class="p">].</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">,</span> <span class="n" style="color: #333;">target_idx</span><span class="p">,</span> <span class="n" style="color: #333;">qlen</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/bfb476e4a522c45a09fba4c73f6e0962135133ce#76d5a97c09cca591280144de40f9c04a5ec57ef7"><strong>src/basic/basic.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +29,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../util/util.h"</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../stats/standard_matrix.h"</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">version_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.0.1<span class="idiff left right">2</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">version_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.0.1<span class="idiff left right">3</span>"</span><span class="p">;</span></span>
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"diamond"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="n" style="color: #333;">Align_mode</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Align_mode</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">mode</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/bfb476e4a522c45a09fba4c73f6e0962135133ce#da280a51d91809345347036c4e31920b2c744ab7"><strong>src/basic/const.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,7 +25,7 @@ struct Const</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"> <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"> <span class="n" style="color: #333;">build_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15<span class="idiff left right">0</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"> <span class="n" style="color: #333;">build_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15<span class="idiff left right">1</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef SINGLE_THREADED</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"> <span class="n" style="color: #333;">seedp_bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/bfb476e4a522c45a09fba4c73f6e0962135133ce#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">@@ -337,6 +337,7 @@ Hsp traceback(Sequence *query, Strand strand, int dna_len, const Banded3FrameSwi</td>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">Hsp</span> <span class="n" style="color: #333;">out</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="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">swipe_target</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">target_idx</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">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;">int_score</span><span class="p">(</span><span class="n" style="color: #333;">max_score</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">cbs_matrix_scale</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">bit_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score_matrix</span><span class="p">.</span><span class="n" style="color: #333;">bitscore</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">transcript</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><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;">out</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">transcript_len_estimate</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="378" style="width: 35px; color: rgba(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="379" style="width: 35px; color: rgba(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">@@ -378,6 +379,7 @@ Hsp traceback(Sequence *query, Strand strand, int dna_len, const Banded3FrameSwi</td>
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378
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i1</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">d_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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379
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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;">out</span><span class="p">.</span><span class="n" style="color: #333;">swipe_target</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">target_idx</span><span class="p">;</span></span>
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380
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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;">out</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">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;">int_score</span><span class="p">(</span><span class="n" style="color: #333;">max_score</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">cbs_matrix_scale</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">bit_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score_matrix</span><span class="p">.</span><span class="n" style="color: #333;">bitscore</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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381
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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382
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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;">out</span><span class="p">.</span><span class="n" style="color: #333;">query_range</span><span class="p">.</span><span class="n" style="color: #333;">end_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">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;">i0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">max_col</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">dp</span><span class="p">.</span><span class="n" style="color: #333;">band</span><span class="p">()</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="mi" style="color: #099;">2</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">query</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">length</span><span class="p">());</span></span>
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383
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">query_range</span><span class="p">.</span><span class="n" style="color: #333;">begin_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">query_range</span><span class="p">.</span><span class="n" style="color: #333;">end_</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">j0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">max_col</span><span class="p">),</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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