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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>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/commit/7115000b993951a6922ba64a059a34edb4ec5b1e">7115000b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-20T16:19:23Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">clean up better
</pre>
</li>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
debian/patches/simde
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
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<h4>Changes:</h4>
<li id="4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
<a href="https://salsa.debian.org/med-team/last-align/commit/7115000b993951a6922ba64a059a34edb4ec5b1e#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">@@ -273,3 +273,146 @@</td>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="diff"> $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $(MBOBJ)</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"> .SUFFIXES:</span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="p">@@ -147,9 +149,17 @@</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> mv m makefile</span>
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<td class="diff-line-num new new_line" data-linenumber="278" 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="LC278" class="line" lang="diff"> Alignment.o Alignment.o8: Alignment.cc Alignment.hh ScoreMatrixRow.hh SegmentPair.hh \</span>
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<td class="diff-line-num new new_line" data-linenumber="279" 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="LC279" class="line" lang="diff"> mcf_gap_costs.hh Alphabet.hh Centroid.hh GappedXdropAligner.hh \</span>
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<td class="diff-line-num new new_line" data-linenumber="280" 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="LC280" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mcf_contiguous_queue.hh mcf_simd.hh OneQualityScoreMatrix.hh \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="281" 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="LC281" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mcf_substitution_matrix_stats.hh GeneticCode.hh GreedyXdropAligner.hh \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="282" 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="LC282" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- TwoQualityScoreMatrix.hh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="283" 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="LC283" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mcf_contiguous_queue.hh mcf_simd.hh ../debian/include/simde/x86/avx2.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="284" 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="LC284" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/avx.h ../debian/include/simde/x86/sse.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="285" 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="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/mmx.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="286" 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="LC286" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../simde-common.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../hedley.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../check.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="289" 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="LC289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../simde-arch.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="290" 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="LC290" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="291" 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="LC291" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="292" 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="LC292" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ OneQualityScoreMatrix.hh mcf_substitution_matrix_stats.hh GeneticCode.hh \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="293" 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="LC293" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ GreedyXdropAligner.hh TwoQualityScoreMatrix.hh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="294" 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">
294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> AlignmentPot.o AlignmentPot.o8: AlignmentPot.cc AlignmentPot.hh Alignment.hh \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="295" 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">
295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> ScoreMatrixRow.hh SegmentPair.hh mcf_gap_costs.hh</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="296" 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">
296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> AlignmentWrite.o AlignmentWrite.o8: AlignmentWrite.cc Alignment.hh ScoreMatrixRow.hh \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="p">@@ -160,28 +170,77 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="298" 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">
298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"> Alphabet.hh</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="299" 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">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> Alphabet.o Alphabet.o8: Alphabet.cc Alphabet.hh</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="300" 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">
300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> Centroid.o Centroid.o8: Centroid.cc Centroid.hh GappedXdropAligner.hh \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="301" 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">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mcf_contiguous_queue.hh mcf_simd.hh ScoreMatrixRow.hh mcf_gap_costs.hh \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="302" 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">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SegmentPair.hh OneQualityScoreMatrix.hh mcf_substitution_matrix_stats.hh \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="303" 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">
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;">+ mcf_contiguous_queue.hh mcf_simd.hh ../debian/include/simde/x86/avx2.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="304" 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">
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;">+ ../debian/include/simde/x86/avx.h ../debian/include/simde/x86/sse.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="305" 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">
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;">+ ../debian/include/simde/x86/mmx.h \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="306" 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">
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;">+ ../debian/include/simde/x86/../simde-common.h \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../hedley.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="308" 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">
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;">+ ../debian/include/simde/x86/../check.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="309" 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">
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;">+ ../debian/include/simde/x86/../simde-arch.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="311" 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">
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;">+ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ScoreMatrixRow.hh mcf_gap_costs.hh SegmentPair.hh \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="313" 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">
313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ OneQualityScoreMatrix.hh mcf_substitution_matrix_stats.hh \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="314" 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">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> GappedXdropAlignerInl.hh</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="315" 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">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> CyclicSubsetSeed.o CyclicSubsetSeed.o8: CyclicSubsetSeed.cc CyclicSubsetSeed.hh \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="316" 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">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> CyclicSubsetSeedData.hh zio.hh mcf_zstream.hh stringify.hh</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="317" 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">
317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> DiagonalTable.o DiagonalTable.o8: DiagonalTable.cc DiagonalTable.hh</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="318" 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">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> GappedXdropAligner.o GappedXdropAligner.o8: GappedXdropAligner.cc GappedXdropAligner.hh \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="319" 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">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mcf_contiguous_queue.hh mcf_simd.hh ScoreMatrixRow.hh \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="320" 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">
320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- GappedXdropAlignerInl.hh</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="321" 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">
321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mcf_contiguous_queue.hh mcf_simd.hh ../debian/include/simde/x86/avx2.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="322" 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">
322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/avx.h ../debian/include/simde/x86/sse.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="323" 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">
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;">+ ../debian/include/simde/x86/mmx.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="324" 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">
324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../simde-common.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="325" 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">
325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../hedley.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="326" 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">
326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../check.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="327" 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">
327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../simde-arch.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="328" 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">
328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="329" 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">
329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="330" 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">
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;">+ ScoreMatrixRow.hh GappedXdropAlignerInl.hh</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="331" 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">
331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> GappedXdropAligner2qual.o GappedXdropAligner2qual.o8: GappedXdropAligner2qual.cc \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="332" 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">
332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_simd.hh \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="333" 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">
333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/avx2.h ../debian/include/simde/x86/avx.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="334" 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">
334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/sse.h ../debian/include/simde/x86/mmx.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="335" 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">
335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../simde-common.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="336" 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">
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;">+ ../debian/include/simde/x86/../hedley.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="337" 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">
337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../check.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="338" 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">
338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../simde-arch.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="339" 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">
339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="340" 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">
340
</td>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="341" 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">
341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> ScoreMatrixRow.hh GappedXdropAlignerInl.hh TwoQualityScoreMatrix.hh \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="342" 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">
342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> mcf_substitution_matrix_stats.hh</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="343" 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">
343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> GappedXdropAligner3frame.o GappedXdropAligner3frame.o8: GappedXdropAligner3frame.cc \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="344" 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">
344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_simd.hh \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="345" 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">
345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/avx2.h ../debian/include/simde/x86/avx.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="346" 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">
346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/sse.h ../debian/include/simde/x86/mmx.h \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="347" 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">
347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../simde-common.h \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="348" 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">
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;">+ ../debian/include/simde/x86/../hedley.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="349" 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">
349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../check.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="350" 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">
350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../simde-arch.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="351" 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">
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;">+ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="352" 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">
352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="353" 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">
353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> ScoreMatrixRow.hh GappedXdropAlignerInl.hh</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="354" 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">
354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> GappedXdropAligner3framePssm.o GappedXdropAligner3framePssm.o8: GappedXdropAligner3framePssm.cc \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="355" 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">
355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_simd.hh \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="356" 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">
356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/avx2.h ../debian/include/simde/x86/avx.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="357" 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">
357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/sse.h ../debian/include/simde/x86/mmx.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="358" 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">
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;">+ ../debian/include/simde/x86/../simde-common.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="359" 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">
359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../hedley.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="360" 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">
360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../check.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="361" 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">
361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../simde-arch.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="362" 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">
362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="363" 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">
363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="364" 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">
364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> ScoreMatrixRow.hh GappedXdropAlignerInl.hh</span>
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<td class="diff-line-num new new_line" data-linenumber="365" 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">
365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> GappedXdropAlignerPssm.o GappedXdropAlignerPssm.o8: GappedXdropAlignerPssm.cc GappedXdropAligner.hh \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="366" 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">
366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mcf_contiguous_queue.hh mcf_simd.hh ScoreMatrixRow.hh \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="367" 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">
367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- GappedXdropAlignerInl.hh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="368" 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">
368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mcf_contiguous_queue.hh mcf_simd.hh ../debian/include/simde/x86/avx2.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="369" 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">
369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/avx.h ../debian/include/simde/x86/sse.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="370" 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">
370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/mmx.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="371" 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">
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;">+ ../debian/include/simde/x86/../simde-common.h \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="372" 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">
372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../hedley.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="373" 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">
373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../check.h \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="374" 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">
374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../simde-arch.h \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="375" 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">
375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="377" 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">
377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ScoreMatrixRow.hh GappedXdropAlignerInl.hh</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="378" 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">
378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> GeneticCode.o GeneticCode.o8: GeneticCode.cc GeneticCode.hh GeneticCodeData.hh \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="379" 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">
379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> Alphabet.hh zio.hh mcf_zstream.hh</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="380" 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">
380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> GreedyXdropAligner.o GreedyXdropAligner.o8: GreedyXdropAligner.cc GreedyXdropAligner.hh \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="381" 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">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="p">@@ -205,8 +264,9 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="382" 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">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> ScoreMatrixRow.hh qualityScoreUtil.hh stringify.hh</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="383" 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">
383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"> QualityPssmMaker.o QualityPssmMaker.o8: QualityPssmMaker.cc QualityPssmMaker.hh \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="384" 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">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> ScoreMatrixRow.hh qualityScoreUtil.hh stringify.hh</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="385" 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">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ScoreMatrix.o ScoreMatrix.o8: ScoreMatrix.cc ScoreMatrix.hh ScoreMatrixData.hh \</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="386" 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">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- qualityScoreUtil.hh stringify.hh zio.hh mcf_zstream.hh</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="387" 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">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ScoreMatrix.o ScoreMatrix.o8: ScoreMatrix.cc ScoreMatrix.hh ScoreMatrixRow.hh \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="388" 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">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ScoreMatrixData.hh qualityScoreUtil.hh stringify.hh zio.hh \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="389" 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">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mcf_zstream.hh</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="390" 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">
390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> SegmentPair.o SegmentPair.o8: SegmentPair.cc SegmentPair.hh</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="391" 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">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> SegmentPairPot.o SegmentPairPot.o8: SegmentPairPot.cc SegmentPairPot.hh SegmentPair.hh</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="392" 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">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"> SubsetMinimizerFinder.o SubsetMinimizerFinder.o8: SubsetMinimizerFinder.cc \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="393" 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">
393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="p">@@ -245,11 +305,20 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="394" 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">
394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> alp/sls_falp_alignment_evaluer.hpp alp/sls_fsa1_pvalues.hpp \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="395" 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">
395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> GeneticCode.hh SubsetMinimizerFinder.hh SubsetSuffixArray.hh \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="396" 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">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> CyclicSubsetSeed.hh Centroid.hh GappedXdropAligner.hh \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="397" 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">
397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mcf_contiguous_queue.hh mcf_simd.hh mcf_gap_costs.hh SegmentPair.hh \</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="398" 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">
398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- AlignmentPot.hh Alignment.hh SegmentPairPot.hh ScoreMatrix.hh \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="399" 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">
399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- TantanMasker.hh tantan.hh DiagonalTable.hh GreedyXdropAligner.hh \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="400" 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">
400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gaplessXdrop.hh gaplessPssmXdrop.hh gaplessTwoQualityXdrop.hh zio.hh \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mcf_zstream.hh threadUtil.hh version.hh</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="402" 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">
402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mcf_contiguous_queue.hh mcf_simd.hh ../debian/include/simde/x86/avx2.h \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="403" 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">
403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/avx.h ../debian/include/simde/x86/sse.h \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="404" 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">
404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/mmx.h \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../simde-common.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="406" 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">
406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../hedley.h \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="407" 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">
407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../check.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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="408" 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">
408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/../simde-arch.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="409" 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">
409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="410" 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">
410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="411" 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">
411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mcf_gap_costs.hh SegmentPair.hh AlignmentPot.hh Alignment.hh \</span></span>
</pre>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SegmentPairPot.hh ScoreMatrix.hh TantanMasker.hh tantan.hh \</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DiagonalTable.hh GreedyXdropAligner.hh gaplessXdrop.hh \</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ gaplessPssmXdrop.hh gaplessTwoQualityXdrop.hh zio.hh mcf_zstream.hh \</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ threadUtil.hh version.hh</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> lastdb.o lastdb.o8: lastdb.cc last.hh Alphabet.hh MultiSequence.hh \</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"> ScoreMatrixRow.hh VectorOrMmap.hh Mmap.hh fileMap.hh stringify.hh \</span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"> SequenceFormat.hh qualityScoreUtil.hh LastdbArguments.hh \</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/last-align/commit/7115000b993951a6922ba64a059a34edb4ec5b1e#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">@@ -37,14 +37,16 @@ ifeq (amd64,$(DEB_HOST_ARCH))</td>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> mkdir -p $(libexecdir)</span>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> $(MAKE) -j$(NUMJOBS) all SFX=-$${SIMD} CXXFLAGS="$(CXXFLAGS) -m$$SIMD" CFLAGS="$(CFLAGS) -m$$SIMD" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)" ; \</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> rm src/*.o? ; \</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> find src -name '*.o' -delete ; \</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> find src -name '*.o8' -delete ; \</span>
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41
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> done</span>
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42
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">else ifeq (i386,$(DEB_HOST_ARCH))</span>
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43
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> mkdir -p $(prefix)</span>
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44
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> mkdir -p $(libexecdir)</span>
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45
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> for SIMD in ssse3 sse3 sse2 sse mmx; do \</span>
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46
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> $(MAKE) -j$(NUMJOBS) all SFX=-$${SIMD} CXXFLAGS="$(CXXFLAGS) -m$$SIMD" CFLAGS="$(CFLAGS) -m$$SIMD" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)" ; \</span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> rm src/*.o? ; \</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> find src -name '*.o' -delete ; \</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> find src -name '*.o8' -delete ; \</span>
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48
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> done</span>
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49
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> $(MAKE) -j$(NUMJOBS) all SFX=-plain CXXFLAGS="$(CXXFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">else</span>
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