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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/diamond-aligner">Debian Med / diamond-aligner</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/diamond-aligner/commit/4de9951f3b1ea2b9200c7b058cc34b312350a052">4de9951f</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-01-13T18:23:54+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">patch to enable non-x86 builds again (no -msse, etc..)
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#1a7530a63305f1b18ca6f436ae59393c470803b9">
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+
debian/patches/multi_arch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/4de9951f3b1ea2b9200c7b058cc34b312350a052#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">diamond-aligner (0.9.29+dfsg-3) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * patch to enable non-x86 builds again (no -msse, etc..)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 13 Jan 2020 17:11:06 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">diamond-aligner (0.9.29+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> [ Frédéric Bonnard ]</span>
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<li id="1a7530a63305f1b18ca6f436ae59393c470803b9">
<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/4de9951f3b1ea2b9200c7b058cc34b312350a052#1a7530a63305f1b18ca6f436ae59393c470803b9"><strong>debian/patches/multi_arch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: handle non-x86 builds again</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- diamond-aligner.orig/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ diamond-aligner/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -5,6 +5,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> option(EXTRA "EXTRA" OFF)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> option(STATIC_LIBGCC "STATIC_LIBGCC" OFF)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> option(STATIC_LIBSTDC++ "STATIC_LIBSTDC++" OFF)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+option(X86 "X86" ON)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> IF(STATIC_LIBSTDC++)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -static-libstdc++")</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -61,9 +62,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> add_library(arch_generic OBJECT ${DISPATCH_OBJECTS})</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> target_compile_options(arch_generic PUBLIC -DDISPATCH_ARCH=ARCH_GENERIC)</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if(X86)</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> add_library(arch_sse4_1 OBJECT ${DISPATCH_OBJECTS})</span>
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19
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<pre style="margin: 0;">+<span id="LC19" 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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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if(X86)</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> add_executable(diamond $<TARGET_OBJECTS:arch_generic></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> $<TARGET_OBJECTS:arch_sse4_1></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> src/run/main.cpp</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -149,6 +153,91 @@</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> src/lib/tantan/LambdaCalculator.cc</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> src/data/taxonomy_filter.cpp</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> )</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;">+else()</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+add_executable(diamond $<TARGET_OBJECTS:arch_generic></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;">+ src/run/main.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/basic/config.cpp</span></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;">+ src/basic/score_matrix.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/blast/blast_filter.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/blast/blast_seg.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;">+ src/blast/sm_blosum45.c</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/blast/sm_blosum50.c</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/blast/sm_blosum62.c</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/blast/sm_blosum80.c</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/blast/sm_blosum90.c</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/blast/sm_pam30.c</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/blast/sm_pam70.c</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/blast/sm_pam250.c</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/data/queries.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/data/reference.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/data/seed_histogram.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/output/daa_record.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/command_line_parser.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/seq_file_format.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/util.cpp </span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/Timer.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/basic/basic.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/basic/hssp.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/dp/ungapped_align.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/run/tools.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/dp/greedy_align.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/output/output_format.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/output/join_blocks.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/data/frequent_seeds.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/align/query_mapper.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;">+ src/output/blast_tab_format.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/dp/padded_banded_sw.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/dp/needleman_wunsch.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/output/blast_pairwise_format.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/dp/comp_based_stats.cpp</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/run/double_indexed.cpp</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;">+ src/output/sam_format.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/align/align.cpp</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/search/setup.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/dp/diag_scores.cpp</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/data/taxonomy.cpp</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/lib/tantan/tantan.cc</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/basic/masking.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/dp/banded_sw.cpp</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/data/seed_set.cpp</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;">+ src/util/simd.cpp</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/output/taxon_format.cpp</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/output/view.cpp</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/output/output_sink.cpp</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/output/target_culling.cpp</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/align/greedy_pipeline.cpp</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/align/swipe_pipeline.cpp</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;">+ src/align/banded_swipe_pipeline.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/data/ref_dictionary.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/io/compressed_stream.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/io/deserializer.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/io/file_sink.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/io/file_source.cpp</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/io/input_file.cpp</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/io/input_stream_buffer.cpp</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/io/output_file.cpp</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/io/output_stream_buffer.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/io/serializer.cpp</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;">+ src/util/io/temp_file.cpp</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/io/text_input_file.cpp</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/data/taxon_list.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/data/taxonomy_nodes.cpp</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/algo/MurmurHash3.cpp</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/search/stage0.cpp</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/data/seed_array.cpp</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/output/paf_format.cpp</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;">+ src/util/system/system.cpp</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/run/cluster.cpp</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/algo/greedy_vortex_cover.cpp</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/algo/greedy_vortex_cover_weighted.cpp</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/sequence/sequence.cpp</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/tools/tsv_record.cpp</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;">+ src/tools/tools.cpp</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/system/getRSS.cpp</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/util/math/sparse_matrix.cpp</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/lib/tantan/LambdaCalculator.cc</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/data/taxonomy_filter.cpp</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> </span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> if(EXTRA)</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> target_sources(diamond</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- diamond-aligner.orig/src/tools/benchmark.cpp</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ diamond-aligner/src/tools/benchmark.cpp</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="p">@@ -92,6 +92,7 @@</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> }</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"> </span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#ifdef __SSE__</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> void benchmark_transpose() {</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> static const size_t n = 100000000llu;</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> static char in[256], out[256];</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="p">@@ -103,6 +104,7 @@</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> }</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> cout << "Matrix transpose 16x16 bytes:\t" << (double)duration_cast<std::chrono::nanoseconds>(high_resolution_clock::now() - t1).count() / (n * 256) * 1000 << " ps/Letter" << endl;</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> </span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> #ifdef __SSE2__</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> void swipe_cell_update() {</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="p">@@ -169,7 +171,9 @@</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> #ifdef __SSSE3__</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> benchmark_ungapped_sse(s1, s2);</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> #endif</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#ifdef __SSE__</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> benchmark_transpose();</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> #ifdef __SSE2__</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> banded_swipe(s1, s2);</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> swipe_cell_update();</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="p">@@ -179,4 +183,4 @@</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> #endif</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> }</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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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}}</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" 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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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}}</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- diamond-aligner.orig/src/util/simd.h</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ diamond-aligner/src/util/simd.h</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="p">@@ -53,6 +53,7 @@</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> enum Flags { SSSE3 = 1, POPCNT = 2, SSE4_1 = 4 };</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> Arch arch();</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> </span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#ifdef __SSE__</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> #define DECL_DISPATCH(ret, name, param) namespace ARCH_GENERIC { ret name param; }\</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> namespace ARCH_SSE4_1 { ret name param; }\</span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> inline std::function<decltype(ARCH_GENERIC::name)> dispatch_target_##name() {\</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="p">@@ -61,9 +62,17 @@</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> default: return ARCH_GENERIC::name;\</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> }}\</span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> const std::function<decltype(ARCH_GENERIC::name)> name = dispatch_target_##name();</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" 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="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define DECL_DISPATCH(ret, name, param) namespace ARCH_GENERIC { ret name param; }\</span></span>
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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;">+namespace ARCH_SSE4_1 { ret name param; }\</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+inline std::function<decltype(ARCH_GENERIC::name)> dispatch_target_##name() {\</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+return ARCH_GENERIC::name;\</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" 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="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const std::function<decltype(ARCH_GENERIC::name)> name = dispatch_target_##name();</span></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> std::string features();</span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> };</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" 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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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;">+#endif</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- diamond-aligner.orig/src/util/simd/transpose.h</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ diamond-aligner/src/util/simd/transpose.h</span></span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="p">@@ -21,6 +21,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> #include "../simd.h"</span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#ifdef __SSE__</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> inline void merge(__m128i &first, __m128i &second, __m128i &temp)</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"> temp = first;</span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="p">@@ -118,4 +120,5 @@</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> merge_fast_write(xmm0, xmm1, 0, 1, xmm9, (__m128i*)out);</span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif /* __SSE__ */</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> #endif /* TRANSPOSE_H_ */</span></pre>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/4de9951f3b1ea2b9200c7b058cc34b312350a052#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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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">multi_arch</span></pre>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/commit/4de9951f3b1ea2b9200c7b058cc34b312350a052#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -8,13 +8,15 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all</td>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">MSSSSE3=$(shell if [ `dpkg-architecture -qDEB_BUILD_ARCH` = 'amd64' ] ; then echo "-mssse3" ; fi)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">ifeq (,$(filter(DEB_HOST_ARCH),i386 amd64))</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> EXTRA=-DX86=OFF</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">endif</span>
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<td class="diff-line-num old_line" data-linenumber="12" 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">
12
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<td class="diff-line-num new_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">
14
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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="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">
13
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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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">%:</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">
14
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<td class="diff-line-num new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> dh $@</span>
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15
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<td class="diff-line-num new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> dh_auto_configure -- $(EXTRA)</span>
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<td class="diff-line-num new old_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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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="16" 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">
16
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">override_dh_compress:</span>
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<td class="diff-line-num old_line" data-linenumber="17" 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">
17
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> dh_compress --exclude=.pdf</span></pre>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">build_simple:</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> MSSSSE3=$(MSSSSE3) build_simple.sh</span></pre>
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