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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/minimap2">Debian Med / minimap2</a>
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<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/minimap2/-/commit/0bc2dbcf576c2554da3acbf1fa4ccfc1a60ddb44">0bc2dbcf</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2021-11-07T19:24:38+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add SIMDe bits to python-sse4-arch.patch ; adjust SIMDe patch
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#d35b47736da2c4a1f6a0595ac0a6e0fc4759d32c">
debian/patches/python-sse4-arch.patch
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<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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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/minimap2/-/commit/0bc2dbcf576c2554da3acbf1fa4ccfc1a60ddb44#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">minimap2 (2.22+dfsg-3) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add SIMDe bits to python-sse4-arch.patch ; adjust SIMDe patch.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #998015</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> Sun, 07 Nov 2021 19:23:30 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">minimap2 (2.22+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team upload</span>
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<li id="d35b47736da2c4a1f6a0595ac0a6e0fc4759d32c">
<a href="https://salsa.debian.org/med-team/minimap2/-/commit/0bc2dbcf576c2554da3acbf1fa4ccfc1a60ddb44#d35b47736da2c4a1f6a0595ac0a6e0fc4759d32c"><strong>debian/patches/python-sse4-arch.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,12 +5,28 @@ Description: Only pass -msse4.1 to the compiler on amd64</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- minimap2.orig/setup.py</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ minimap2/setup.py</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -16,8 +16,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> if platform.machine() in ["aarch64", "arm64"]:</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> include_dirs.append("sse2neon/")</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -5,6 +5,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> from distutils.extension import Extension</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import sys, platform</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import subprocess</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> sys.path.append('python')</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -13,11 +14,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> extra_objects = ['libminimap2.a']</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> include_dirs = ["."]</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if platform.machine() in ["aarch64", "arm64"]:</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- include_dirs.append("sse2neon/")</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else:</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+arch = subprocess.run(["dpkg-architecture", "-qDEB_HOST_ARCH"], capture_output=True, text=True).stdout.strip()</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if arch in ["aarch64", "arm64"]:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-DUSE_SIMDE', '-D__SSE2__', '-DSIMDE_ENABLE_NATIVE_ALIASES', '-fopenmp-simd', '-O3', '-DSIMDE_ENABLE_OPENMP'])</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+elif arch != "amd64":</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ extra_compile_args.extend(['-DKSW_SSE2_ONLY', '-DUSE_SIMDE', '-DSIMDE_ENABLE_NATIVE_ALIASES', '-fopenmp-simd', '-O3', '-DSIMDE_ENABLE_OPENMP'])</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> def readme():</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> with open('python/README.rst') as f:</span></pre>
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<li id="4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
<a href="https://salsa.debian.org/med-team/minimap2/-/commit/0bc2dbcf576c2554da3acbf1fa4ccfc1a60ddb44#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- minimap2.orig/Makefile.simde</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ minimap2/Makefile.simde</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">@@ -1,8 +1,<span class="idiff left right">9</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -1,8 +1,<span class="idiff left right">8</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CPPFLAGS= -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-INCLUDES= -Ilib/simde</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o map.o format.o pe.o seed.o esterr.o splitidx.o \</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS+= -g -Wall -O2 -Wc++-compat #-Wextra</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CPPFLAGS+= -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS+= -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+INCLUDES=</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o \</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> PROG= minimap2</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> PROG_EXTRA= sdust minimap2-lite</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> LIBS= -lm -lz -lpthread</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -37,28 +3<span class="idiff left right">8</span>,27 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -37,28 +3<span class="idiff left right">7</span>,27 @@</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> extra:all $(PROG_EXTRA)</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> minimap2:main.o libminimap2.a</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,14 +55,13 @@</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> # other non-file targets</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="p">@@ -80,<span class="idiff left right">10 +80</span>,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="p">@@ -80,<span class="idiff left right">9 +79</span>,6 @@</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> index.o: kthread.h bseq.h minimap.h mmpriv.h kseq.h kvec.h kalloc.h khash.h</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> index.o: ksort.h</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> kalloc.o: kalloc.h</span>
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63
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_extd2_sse.o: ksw2.h kalloc.h</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_exts2_sse.o: ksw2.h kalloc.h</span></span>
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_extz2_sse.o: ksw2.h kalloc.h</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span>ksw2_ll_sse.o: ksw2.h kalloc.h</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="idiff left right"> </span>ksw2_ll_sse.o: ksw2.h kalloc.h</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> kthread.o: kthread.h</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> main.o: bseq.h minimap.h mmpriv.h kseq.h ketopt.h</span></pre>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"> map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h kseq.h</span></pre>
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<a href="https://salsa.debian.org/med-team/minimap2/-/commit/0bc2dbcf576c2554da3acbf1fa4ccfc1a60ddb44#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">@@ -15,7 +15,7 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> rm -f tex/minimap2.aux tex/minimap2.bbl tex/minimap2.blg tex/minimap2.log tex/minimap2.out tex/minimap2.pdf</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> rm -f libminimap2.a</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">ifeq (,$(filter $(DEB_HOST_ARCH_CPU),amd64))</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">ifeq (,$(filter $(DEB_HOST_ARCH_CPU),amd64<span class="idiff left right"> i386</span>))</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">build_vars = -f Makefile.simde</span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">export DEB_CFLAGS_MAINT_APPEND += -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP</span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">endif</span>
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