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<h3>
Andreas Tille pushed to branch master
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/75cdd3e5941ad035716ce33049cf877c56379283">75cdd3e5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-04-29T19:50:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed missing definition
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/b4966d14731fb449b11bfc3aa010afb5ce6710eb">b4966d14</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-04-30T21:37:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed compiler error, unsigned char errors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/135698a63fdae033b79c698040740332825ea2c2">135698a6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-04-30T21:43:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upstream says diamond-aligner does not run on 32bit systems
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/88b91b35667da03fe23ce867a386507859914f33">88b91b35</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-04-30T21:46:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#84c3518864033ac71f83a5371bb659ebf76d0164">
<span class="new-file">
+
debian/patches/63b3e686f41272851a87c632441ba8c6484a2fe2.patch
</span>
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</li>
<li class="file-stats">
<a href="#7eeed8553b6a575efdf8a4ca5f7897236a178e14">
<span class="new-file">
+
debian/patches/f5daf92d3ece50ebb0c0a5f9b4133769347ec55b.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/diamond-aligner/-/compare/eebe9008a9acb84672a00fd5759ac2455a218274...88b91b35667da03fe23ce867a386507859914f33#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">diamond-aligner (0.9.32-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Fixed different build issues</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> * Upstream says diamond-aligner does not run on 32bit systems</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> https://github.com/bbuchfink/diamond/issues/347#issuecomment-622051316</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 30 Apr 2020 21:43:33 +0200</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">diamond-aligner (0.9.32-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(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="LC11" class="line" lang="plaintext"> * New upstream version</span>
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</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/diamond-aligner/-/compare/eebe9008a9acb84672a00fd5759ac2455a218274...88b91b35667da03fe23ce867a386507859914f33#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ Homepage: https://github.com/bbuchfink/diamond</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Package: diamond-aligner</span>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num new old_line" data-linenumber="17" 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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Architecture: any<span class="idiff left right">-amd64 arm64 mips64el ppc64el s390x ia64 ppc64 riscv64 sh4 sparc64</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> ${misc:Depends}</span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Recommends: med-config (>= 2.1)</span>
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<li id="84c3518864033ac71f83a5371bb659ebf76d0164">
<a href="https://salsa.debian.org/med-team/diamond-aligner/-/compare/eebe9008a9acb84672a00fd5759ac2455a218274...88b91b35667da03fe23ce867a386507859914f33#84c3518864033ac71f83a5371bb659ebf76d0164"><strong>debian/patches/63b3e686f41272851a87c632441ba8c6484a2fe2.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From 63b3e686f41272851a87c632441ba8c6484a2fe2 Mon Sep 17 00:00:00 2001</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Benjamin Buchfink <buchfink@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Date: Thu, 30 Apr 2020 16:35:49 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Subject: [PATCH] Fixed compiler error, unsigned char errors.</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> CMakeLists.txt | 1 +</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> src/basic/basic.cpp | 14 ----------</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> src/basic/masking.cpp | 4 +--</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> src/basic/masking.h | 4 +--</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> src/basic/reduction.h | 6 ++--</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> src/basic/score_matrix.cpp | 57 +++++++++++++++-----------------------</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> src/basic/score_matrix.h | 12 ++++----</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> src/basic/value.cpp | 16 ++++++++++-</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> src/basic/value.h | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> src/dp/score_vector_int8.h | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> src/search/stage2.cpp | 2 ++</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> src/util/tantan.cpp | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> src/util/tantan.h | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> 13 files changed, 57 insertions(+), 67 deletions(-)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff">diff --git a/CMakeLists.txt b/CMakeLists.txt</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gh" style="color: #999;">index 8eb8f16b..59b92b79 100644</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -87,6 +87,7 @@</span> if(X86)</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> add_library(arch_sse4_1 OBJECT ${DISPATCH_OBJECTS})</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> if (${CMAKE_CXX_COMPILER_ID} STREQUAL MSVC)</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> target_compile_options(arch_sse4_1 PUBLIC -DDISPATCH_ARCH=ARCH_SSE4_1 -D__SSSE3__ -D__SSE4_1__ -D__POPCNT__)</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #target_compile_options(arch_sse4_1 PUBLIC -DDISPATCH_ARCH=ARCH_SSE4_1)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> else()</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> target_compile_options(arch_sse4_1 PUBLIC -DDISPATCH_ARCH=ARCH_SSE4_1 -mssse3 -mpopcnt -msse4.1)</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> endif()</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/basic/basic.cpp b/src/basic/basic.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gh" style="color: #999;">index 508327cd..3e546e45 100644</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/basic/basic.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/basic/basic.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -28,20 +28,6 @@</span> const char* Const::version_string = "0.9.32";</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> const char* Const::program_name = "diamond";</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> const char* Const::id_delimiters = " \a\b\f\n\r\t\v\1";</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Value_traits::Value_traits(const char *alphabet, Letter mask_char, const char *ignore) :</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alphabet(alphabet),</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alphabet_size((unsigned)strlen(alphabet)),</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mask_char(mask_char),</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- from_char(Char_representation((unsigned)alphabet_size, alphabet, mask_char, ignore))</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-{}</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-const char Char_representation::invalid = '\xff';</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-const Value_traits amino_acid_traits(AMINO_ACID_ALPHABET, 23, "UO-");</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-const Value_traits nucleotide_traits("ACGTN", 4, "MRWSYKVHDBX");</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Value_traits value_traits(amino_acid_traits);</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Value_traits input_value_traits(amino_acid_traits);</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> Align_mode::Align_mode(unsigned mode) :</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> mode(mode)</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/basic/masking.cpp b/src/basic/masking.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gh" style="color: #999;">index ddbd801e..5ac76c09 100644</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/basic/masking.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/basic/masking.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -26,7 +26,7 @@</span> along with this program. If not, see <http://www.gnu.org/licenses/>.</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> using namespace std;</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> unique_ptr<Masking> Masking::instance;</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-const uint8_t Masking::bit_mask = 128;</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const int8_t Masking::bit_mask = (int8_t)128;</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> Masking::Masking(const Score_matrix &score_matrix)</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="p">@@ -42,7 +42,7 @@</span> Masking::Masking(const Score_matrix &score_matrix)</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> const double lambda = lc.lambda(); // 0.324032</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> for (unsigned i = 0; i < size; ++i) {</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> mask_table_x_[i] = value_traits.mask_char;</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mask_table_bit_[i] = (uint8_t)i | bit_mask;</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mask_table_bit_[i] = (int8_t)i | bit_mask;</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> for (unsigned j = 0; j < size; ++j)</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> if (i < n && j < n) {</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> likelihoodRatioMatrixf_[i][j] = (float)exp(lambda * score_matrix(i, j));</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/basic/masking.h b/src/basic/masking.h</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gh" style="color: #999;">index 24e872d9..dcc5db75 100644</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/basic/masking.h</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/basic/masking.h</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="p">@@ -34,11 +34,11 @@</span> struct Masking</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> return *instance;</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> static std::unique_ptr<Masking> instance;</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- static const uint8_t bit_mask;</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ static const int8_t bit_mask;</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> private:</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> enum { size = 64 };</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> float likelihoodRatioMatrixf_[size][size], *probMatrixPointersf_[size];</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char mask_table_x_[size], mask_table_bit_[size];</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Letter mask_table_x_[size], mask_table_bit_[size];</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> size_t mask_seqs(Sequence_set &seqs, const Masking &masking, bool hard_mask = true);</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/basic/reduction.h b/src/basic/reduction.h</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gh" style="color: #999;">index 54e36431..768fe59d 100644</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/basic/reduction.h</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/basic/reduction.h</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="p">@@ -76,7 +76,7 @@</span> struct Reduction</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> return map_[a];</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> }</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> </span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const char* map8() const</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ const Letter* map8() const</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> {</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> return map8_;</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> }</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="p">@@ -107,9 +107,9 @@</span> struct Reduction</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> unsigned map_[256];</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> #ifdef _MSC_VER</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __declspec(align(16)) char map8_[256];</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ __declspec(align(16)) Letter map8_[256];</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> #else</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char map8_[256] __attribute__((aligned(16)));</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Letter map8_[256] __attribute__((aligned(16)));</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> #endif</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> unsigned size_;</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> uint64_t bit_size_;</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/basic/score_matrix.cpp b/src/basic/score_matrix.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gh" style="color: #999;">index 1a2357b1..b3ba7eac 100644</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/basic/score_matrix.cpp</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/basic/score_matrix.cpp</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="p">@@ -38,18 +38,6 @@</span> typedef double array_of_8[BLAST_NUM_STAT_VALUES];</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> </span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> const double INT2_MAX = std::numeric_limits<double>::max();</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> </span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-const signed char DNA_scores[5 * 5] = {</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 2, -3, -3, -3, -3,</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -3,2,-3,-3,-3,</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -3,-3,2,-3,-3,</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -3,-3,-3,2,-3,</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -3,-3,-3,-3,2</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-};</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-static array_of_8 dna_values[1] = {</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- { 5, 2, (double)INT2_MAX, 0, 0, 0, 0, 0, 0, 0, 0 }</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-};</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> #define BLOSUM45_VALUES_MAX 14 /**< Number of different combinations supported for BLOSUM45. */</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> static array_of_8 blosum45_values[BLOSUM45_VALUES_MAX] = {</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> { (double)INT2_MAX, (double)INT2_MAX, (double)INT2_MAX, 0.2291, 0.0924, 0.2514, 0.9113, -5.7, 0.641318, 9.611060, 9.611060 },</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="p">@@ -177,7 +165,7 @@</span> struct Matrix_info</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> const char *name;</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> const array_of_8 *constants;</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const char *scores;</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ const signed char *scores;</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> const unsigned count;</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> const int default_gap_open, default_gap_extend;</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> </span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="p">@@ -199,19 +187,18 @@</span> struct Matrix_info</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> return 0;</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> }</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> </span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- static const Matrix_info matrices[9];</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ static const Matrix_info matrices[8];</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> };</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> </span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> const Matrix_info Matrix_info::matrices[] = {</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- { "BLOSUM45", blosum45_values, (const char*)s_Blosum45PSM, BLOSUM45_VALUES_MAX, 14, 2 },</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- { "BLOSUM50", blosum50_values, (const char*)s_Blosum50PSM, BLOSUM50_VALUES_MAX, 13, 2 },</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- { "BLOSUM62", blosum62_values, (const char*)s_Blosum62PSM, BLOSUM62_VALUES_MAX, 11, 1 },</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- { "BLOSUM80", blosum80_values, (const char*)s_Blosum80PSM, BLOSUM80_VALUES_MAX, 10, 1 },</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- { "BLOSUM90", blosum90_values, (const char*)s_Blosum90PSM, BLOSUM90_VALUES_MAX, 10, 1 },</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- { "PAM70", pam70_values, (const char*)s_Pam70PSM, PAM70_VALUES_MAX, 10, 1 },</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- { "PAM250", pam250_values, (const char*)s_Pam250PSM, PAM250_VALUES_MAX, 14, 2 },</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="diff"><span class="gd" style="color: #000; background-color: #fdd;">- { "PAM30", pam30_values, (const char*)s_Pam30PSM, PAM30_VALUES_MAX, 9, 1 },</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="diff"><span class="gd" style="color: #000; background-color: #fdd;">- { "DNA", dna_values, (const char*)DNA_scores, 1, 4, 2 }</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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ { "BLOSUM45", blosum45_values, (const signed char*)s_Blosum45PSM, BLOSUM45_VALUES_MAX, 14, 2 },</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ { "BLOSUM50", blosum50_values, (const signed char*)s_Blosum50PSM, BLOSUM50_VALUES_MAX, 13, 2 },</span></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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ { "BLOSUM62", blosum62_values, (const signed char*)s_Blosum62PSM, BLOSUM62_VALUES_MAX, 11, 1 },</span></span>
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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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ { "BLOSUM80", blosum80_values, (const signed char*)s_Blosum80PSM, BLOSUM80_VALUES_MAX, 10, 1 },</span></span>
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<td class="diff-line-num new new_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">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ { "BLOSUM90", blosum90_values, (const signed char*)s_Blosum90PSM, BLOSUM90_VALUES_MAX, 10, 1 },</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" 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">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ { "PAM70", pam70_values, (const signed char*)s_Pam70PSM, PAM70_VALUES_MAX, 10, 1 },</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" 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">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ { "PAM250", pam250_values, (const signed char*)s_Pam250PSM, PAM250_VALUES_MAX, 14, 2 },</span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ { "PAM30", pam30_values, (const signed char*)s_Pam30PSM, PAM30_VALUES_MAX, 9, 1 }</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> };</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> </span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> Score_matrix::Score_matrix(const string & matrix, int gap_open, int gap_extend, int frameshift, int stop_match_score, uint64_t db_letters):</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="p">@@ -228,21 +215,21 @@</span> Score_matrix::Score_matrix(const string & matrix, int gap_open, int gap_extend,</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> matrix32_(Matrix_info::get(matrix).scores, stop_match_score)</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> { }</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> </span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-char Score_matrix::low_score() const</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+int8_t Score_matrix::low_score() const</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> {</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char low = std::numeric_limits<char>::max();</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (Letter i = 0; i < (char)value_traits.alphabet_size; ++i)</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (Letter j = i + 1; j < (char)value_traits.alphabet_size; ++j)</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- low = std::min(low, (char)this->operator()(i, j));</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int8_t low = std::numeric_limits<int8_t>::max();</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (Letter i = 0; i < (Letter)value_traits.alphabet_size; ++i)</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (Letter j = i + 1; j < (Letter)value_traits.alphabet_size; ++j)</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ low = std::min(low, (int8_t)this->operator()(i, j));</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> return low;</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> }</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> </span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-char Score_matrix::high_score() const</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+int8_t Score_matrix::high_score() const</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> {</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char high = std::numeric_limits<char>::min();</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (Letter i = 0; i < (char)value_traits.alphabet_size; ++i)</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (Letter j = i; j < (char)value_traits.alphabet_size; ++j)</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- high = std::max(high, (char)this->operator()(i, j));</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int8_t high = std::numeric_limits<int8_t>::min();</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (Letter i = 0; i < (Letter)value_traits.alphabet_size; ++i)</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (Letter j = i; j < (Letter)value_traits.alphabet_size; ++j)</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ high = std::max(high, (int8_t)this->operator()(i, j));</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> return high;</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> }</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="p">@@ -264,9 +251,9 @@</span> std::ostream& operator<<(std::ostream& s, const Score_matrix &m)</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> return s;</span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> }</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> </span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-const char* custom_scores(const string &matrix_file)</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const signed char* custom_scores(const string &matrix_file)</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> {</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- static char scores[25 * 25];</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ static signed char scores[25 * 25];</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> string l, s;</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> std::stringstream ss;</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> vector<Letter> pos;</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/basic/score_matrix.h b/src/basic/score_matrix.h</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gh" style="color: #999;">index 02cc710d..9fa132e3 100644</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/basic/score_matrix.h</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/basic/score_matrix.h</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="p">@@ -60,7 +60,7 @@</span> struct Score_matrix</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> return matrix8_.data[(int(a) << 5) + int(b)];</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> }</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> </span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const int* row(char a) const</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ const int* row(Letter a) const</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> {</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> return &matrix32_.data[(int)a << 5];</span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> }</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="p">@@ -106,8 +106,8 @@</span> struct Score_matrix</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> return log(k());</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> }</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> </span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char low_score() const;</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char high_score() const;</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int8_t low_score() const;</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int8_t high_score() const;</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> </span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> int gap_open() const</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> {</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="p">@@ -142,7 +142,7 @@</span> struct Score_matrix</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> struct Scores</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> {</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> Scores() {}</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Scores(const char *scores, int stop_match_score = 1, char bias = 0)</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Scores(const int8_t *scores, int stop_match_score = 1, int8_t bias = 0)</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> {</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> const unsigned n = value_traits.alphabet_size;</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> for (unsigned i = 0; i < 32; ++i)</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="p">@@ -163,7 +163,7 @@</span> struct Score_matrix</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> const double *constants_;</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> string name_;</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> Scores<int8_t> matrix8_;</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char bias_;</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int8_t bias_;</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> Scores<uint8_t> matrix8u_;</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> Scores<int16_t> matrix16_;</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> Scores<int> matrix32_;</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="p">@@ -171,7 +171,7 @@</span> struct Score_matrix</span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> extern Score_matrix score_matrix;</span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-typedef signed char MatrixTable[AMINO_ACID_COUNT*AMINO_ACID_COUNT];</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+typedef int8_t MatrixTable[AMINO_ACID_COUNT*AMINO_ACID_COUNT];</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> extern const MatrixTable s_Blosum45PSM, s_Blosum50PSM, s_Blosum62PSM, s_Blosum80PSM, s_Blosum90PSM, s_Pam250PSM, s_Pam30PSM, s_Pam70PSM;</span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> #endif /* SCORE_MATRIX_H_ */</span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/basic/value.cpp b/src/basic/value.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gh" style="color: #999;">index 3a5169f7..aa350cf9 100644</span></span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/basic/value.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/basic/value.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="p">@@ -3,6 +3,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> #include "value.h"</span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> #include "../util/util.h"</span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const Letter Char_representation::invalid = '\xff';</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> invalid_sequence_char_exception::invalid_sequence_char_exception(char ch) :</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> msg(std::string("Invalid character (") + print_char(ch) + ") in sequence")</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> { }</span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="p">@@ -21,4 +23,16 @@</span> Char_representation::Char_representation(unsigned size, const char* chars, char</span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> data_[(long)tolower(ch)] = mask;</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> ++mask_chars;</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Value_traits::Value_traits(const char* alphabet, Letter mask_char, const char* ignore) :</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ alphabet(alphabet),</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ alphabet_size((unsigned)strlen(alphabet)),</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mask_char(mask_char),</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from_char(Char_representation((unsigned)alphabet_size, alphabet, mask_char, ignore))</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+{}</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const Value_traits amino_acid_traits(AMINO_ACID_ALPHABET, 23, "UO-");</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const Value_traits nucleotide_traits("ACGTN", 4, "MRWSYKVHDBX");</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Value_traits value_traits(amino_acid_traits);</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Value_traits input_value_traits(amino_acid_traits);</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/basic/value.h b/src/basic/value.h</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"><span class="gh" style="color: #999;">index 214eda9b..db6c7c08 100644</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/basic/value.h</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/basic/value.h</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="p">@@ -51,7 +51,7 @@</span> struct Char_representation</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> return data_[(long)c];</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> }</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> private:</span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- static const char invalid;</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ static const Letter invalid;</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> Letter data_[256];</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> };</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> </span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/dp/score_vector_int8.h b/src/dp/score_vector_int8.h</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="gh" style="color: #999;">index 67406fbc..ff7b271a 100644</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dp/score_vector_int8.h</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dp/score_vector_int8.h</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="p">@@ -28,7 +28,7 @@</span> struct score_vector<int8_t></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> {</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> </span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> score_vector():</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- data_(_mm_set1_epi8(std::numeric_limits<char>::min()))</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ data_(_mm_set1_epi8(SCHAR_MIN))</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> {}</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> explicit score_vector(__m128i data):</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/search/stage2.cpp b/src/search/stage2.cpp</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"><span class="gh" style="color: #999;">index 1f2ab6c4..a2df8374 100644</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/search/stage2.cpp</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/search/stage2.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="p">@@ -189,8 +189,10 @@</span> void stage2(const Packed_loc *q,</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> typedef Map<vector<Stage1_hit>::const_iterator, Stage1_hit::Query> Map_t;</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> Map_t map(hits.begin(), hits.end());</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> if (config.fast_stage2) {</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#ifdef __SSE2__</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> for (Map_t::Iterator i = map.begin(); i.valid(); ++i)</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> search_query_offset(q[i.begin()->q], s, i.begin(), i.end(), stats, out, sid, context);</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> }</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> else {</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> for (Map_t::Iterator i = map.begin(); i.valid(); ++i)</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/util/tantan.cpp b/src/util/tantan.cpp</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gh" style="color: #999;">index bdae2b4b..54a7c64d 100644</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/util/tantan.cpp</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/util/tantan.cpp</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="p">@@ -40,7 +40,7 @@</span> void mask(Letter *seq,</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> float p_repeat_end,</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> float repeat_growth,</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> float p_mask,</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const char *mask_table) {</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ const Letter *mask_table) {</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> constexpr int WINDOW = 50, RESERVE = 50000;</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> </span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> thread_local std::array<Array<float, Dynamic, 1>, AMINO_ACID_COUNT> e;</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/util/tantan.h b/src/util/tantan.h</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="gh" style="color: #999;">index 60ab831f..3fd3ecec 100644</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/util/tantan.h</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/util/tantan.h</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="p">@@ -26,7 +26,7 @@</span> along with this program. If not, see <http://www.gnu.org/licenses/>.</span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> namespace Util { namespace tantan {</span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-DECL_DISPATCH(void, mask, (Letter *seq, int len, const float **likelihood_ratio_matrix, float p_repeat, float p_repeat_end, float repeat_decay, float p_mask, const char *maskTable))</span></span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+DECL_DISPATCH(void, mask, (Letter *seq, int len, const float **likelihood_ratio_matrix, float p_repeat, float p_repeat_end, float repeat_decay, float p_mask, const Letter *maskTable))</span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> }}</span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> </span></pre>
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<li id="7eeed8553b6a575efdf8a4ca5f7897236a178e14">
<a href="https://salsa.debian.org/med-team/diamond-aligner/-/compare/eebe9008a9acb84672a00fd5759ac2455a218274...88b91b35667da03fe23ce867a386507859914f33#7eeed8553b6a575efdf8a4ca5f7897236a178e14"><strong>debian/patches/f5daf92d3ece50ebb0c0a5f9b4133769347ec55b.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From f5daf92d3ece50ebb0c0a5f9b4133769347ec55b Mon Sep 17 00:00:00 2001</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Benjamin Buchfink <buchfink@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Date: Wed, 29 Apr 2020 18:02:04 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Subject: [PATCH] Fixed missing definition.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> src/search/sse_dist.h | 8 ++++----</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> 1 file changed, 4 insertions(+), 4 deletions(-)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">diff --git a/src/search/sse_dist.h b/src/search/sse_dist.h</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gh" style="color: #999;">index 44c37d03..54769483 100644</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/search/sse_dist.h</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/search/sse_dist.h</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -116,9 +116,8 @@</span> static inline uint64_t reduced_match(const Letter* q, const Letter* s, int len)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> return (uint64_t)match_block_reduced(q, s) | ((uint64_t)match_block_reduced(q + 16, s + 16) << 16) | ((uint64_t)match_block_reduced(q + 32, s + 32) << 32) | ((uint64_t)match_block_reduced(q + 48, s + 48) << 48);</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE2__</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> static inline uint64_t seed_mask(const Letter* s, int len) {</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#ifdef __SSE2__</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> assert(len <= 64);</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> uint64_t mask = 0;</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> const __m128i m = _mm_set1_epi8(SEED_MASK);</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -130,8 +129,9 @@</span> static inline uint64_t seed_mask(const Letter* s, int len) {</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> if (len < 64)</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> mask &= (1llu << len) - 1;</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> return mask;</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#else</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 0;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> #endif /* SSE_DIST_H_ */</span></pre>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/-/compare/eebe9008a9acb84672a00fd5759ac2455a218274...88b91b35667da03fe23ce867a386507859914f33#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">avoid_unwanted_optimisation.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">82feea2aee5c82e283704b9317cb5e8abc625f90.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">f5daf92d3ece50ebb0c0a5f9b4133769347ec55b.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">63b3e686f41272851a87c632441ba8c6484a2fe2.patch</span></pre>
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