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<h3>
Michael R. Crusoe pushed to branch simde
at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/commit/36ded0b84897a3aecf71494d38e9a2ef5067a7d9">36ded0b8</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2019-12-18T08:11:31Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">patch from upstream simde
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<h4>2 changed files:</h4>
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<a href="#be62058e8e6ab93904815fafc4491680ed01fddb">
debian/include/simde/simde-common.h
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<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
debian/patches/simde
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<h4>Changes:</h4>
<li id="be62058e8e6ab93904815fafc4491680ed01fddb">
<a href="https://salsa.debian.org/med-team/last-align/commit/36ded0b84897a3aecf71494d38e9a2ef5067a7d9#be62058e8e6ab93904815fafc4491680ed01fddb"><strong>debian/include/simde/simde-common.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,10 +62,10 @@</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define SIMDE_CAST_ALIGN(alignment, T, v) \</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> HEDLEY_DIAGNOSTIC_PUSH \</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> _Pragma("clang diagnostic ignored \"-Wcast-align\"") \</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> <span class="idiff left right">HEDLEY_STATIC_CAST(T, v</span>) \</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> <span class="idiff left right">((T) (v)</span>) \</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> HEDLEY_DIAGNOSTIC_POP</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define SIMDE_CAST_ALIGN(alignment, T, v) <span class="idiff left right">HEDLEY_STATIC_CAST(T, v</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define SIMDE_CAST_ALIGN(alignment, T, v) <span class="idiff left right">((T) (v)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if HEDLEY_GCC_HAS_ATTRIBUTE(vector_size,4,6,0)</span></span>
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<li id="4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
<a href="https://salsa.debian.org/med-team/last-align/commit/36ded0b84897a3aecf71494d38e9a2ef5067a7d9#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> #define MCF_SIMD_HH</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"><span class="gd" style="color: #000; background-color: #fdd;">-#include <immintrin.h></span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "debian/include/simde/x86/avx2.h"</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "<span class="idiff left right">../</span>debian/include/simde/x86/avx2.h"</span></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"> namespace mcf {</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,3 +144,45 @@</td>
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144
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="diff"> }</span>
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145
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="diff"> </span>
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146
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="diff"> #endif</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- last-align.orig/src/GappedXdropAligner.cc</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ last-align/src/GappedXdropAligner.cc</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="p">@@ -167,18 +167,13 @@</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> if (isAffine) {</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> for (int i = 0; i < numCells; i += simdLen) {</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> SimdInt s = simdSet(</span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-//#ifdef __AVX2__</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef WANT_AVX2</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> s1[7][s2[-7]],</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> s1[6][s2[-6]],</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> s1[5][s2[-5]],</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> s1[4][s2[-4]],</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> s1[3][s2[-3]],</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> s1[2][s2[-2]],</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> s1[1][s2[-1]],</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> s1[0][s2[-0]]);</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> SimdInt x = simdLoad(x2+i);</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> SimdInt y = simdSub(simdLoad(y1+i), mDelGrowCost);</span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- last-align.orig/src/GappedXdropAlignerPssm.cc</span></span>
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<td class="diff-line-num new new_line" data-linenumber="169" 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">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ last-align/src/GappedXdropAlignerPssm.cc</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="p">@@ -101,18 +101,13 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> if (isAffine) {</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"> for (int i = 0; i < numCells; i += simdLen) {</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"> SimdInt s = simdSet(</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;">-#ifdef __SSE4_1__</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="gd" style="color: #000; background-color: #fdd;">-//#ifdef __AVX2__</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="gd" style="color: #000; background-color: #fdd;">-#ifdef WANT_AVX2</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"> s2[-7][s1[7]],</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"> s2[-6][s1[6]],</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> s2[-5][s1[5]],</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> s2[-4][s1[4]],</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> s2[-3][s1[3]],</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> s2[-2][s1[2]],</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> s2[-1][s1[1]],</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> s2[-0][s1[0]]);</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> SimdInt x = simdLoad(x2+i);</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> SimdInt y = simdSub(simdLoad(y1+i), mDelGrowCost);</span></pre>
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