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<div class="content">
<h3 style="margin-top: 20px; margin-bottom: 10px;">
Étienne Mollier pushed to branch upstream at <a href="https://salsa.debian.org/med-team/vsearch">Debian Med / vsearch</a>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
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<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/vsearch/-/commit/3a5cba1135498d8e665b521e05f206809e3fd9c0">3a5cba11</a></strong>
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<span> by Étienne Mollier </span> <i> at 2025-12-03T22:40:10+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 2.30.1</pre>
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<a href="#b9ec8aebb1af61b37b9a1ee966f6cd8c8aee0d02">
src/bitmap.cc
</a>
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<a href="#ee14bcd900916284957a3bb5078a416b04a52449">
src/bitmap.h
</a>
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src/chimera.cc
</a>
</li>
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<a href="#9552d96e6b96b9a150af98898379b82ac7542c26">
src/chimera.h
</a>
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<a href="#b60f5a030e7b03937c92040341fa0f1aa3a66731">
src/city.cc
</a>
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<a href="#7c09ba6e6c0be90864d70ad16a6f2139767b7de5">
src/city.h
</a>
</li>
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<a href="#05f6b2f8b379638b6f8fb099cd83bb2489591deb">
<span class="deleted-file">
−
src/citycrc.h
</span>
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<li class="file-stats">
<a href="#d79e6705e3db119ee1bb6ad9670fe99b162c13b0">
src/cluster.cc
</a>
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<a href="#d0a709faa909252ae246c0d6c1212099d4cc6343">
src/cluster.h
</a>
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<a href="#0fd044a04525b2a4ea0a87be7b2912b8f1ba6256">
src/cpu.cc
</a>
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src/cpu.h
</a>
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src/cut.cc
</a>
</li>
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<a href="#69543e42a9af20f1730fe3380aec18c2066ef4be">
src/cut.h
</a>
</li>
<li class="file-stats">
<a href="#8fdd0379cd5d3df57faeb8ed82a6423784cead0f">
src/db.cc
</a>
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src/db.h
</a>
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<a href="#ae15476efb5a31ce40a1203b47c2fea4150e53ba">
src/dbhash.cc
</a>
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<a href="#b985b44df11daa336a2d0cad28e584956602ffb5">
src/dbhash.h
</a>
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<a href="#6f9f0505ff192d4ba765bdcc33347f0a6af870f2">
src/dbindex.cc
</a>
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<a href="#fc877ad19029bf6eb726815de883fa4f8a87e687">
src/dbindex.h
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src/derep.cc
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src/derep.h
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<a href="#57b71368ec9b06309c48720267b822b9ca9ff26d">
src/derep_prefix.cc
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<a href="#723aa67f861327e75639753dbffd2f8b75db070a">
src/derep_prefix.h
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src/derep_smallmem.cc
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src/derep_smallmem.h
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src/dynlibs.cc
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src/dynlibs.h
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<a href="#f39ff334aa80788f730c6c2fa78e9dda01843d21">
src/eestats.cc
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<a href="#56cdd7fcb0397dbd312fb7ad3fd6e02ea69723a2">
src/eestats.h
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<a href="#67ef99e491c4bda5d0c47f152cae53d18d7fbcd3">
src/fasta.cc
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<a href="#dce607e2c5a20b2277b76421039058016c3f2150">
src/fasta.h
</a>
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<a href="#aa3c733c98caf29210a1e4b13842055eadbe1eb7">
src/fasta2fastq.cc
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<li class="file-stats">
<a href="#2c5c8d72705bd21f8d9bc7ad9204539eda608147">
src/fasta2fastq.h
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<li class="file-stats">
<a href="#d6ab431461af8e07f1ea378788017353266e8ba2">
src/fastq.cc
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<li class="file-stats">
<a href="#78db7290a5cbafd233799300c3f7a7e51945539d">
src/fastq.h
</a>
</li>
<li class="file-stats">
<a href="#0e29a05efe5c840685f1febb5966511b18e2af83">
src/fastq_chars.cc
</a>
</li>
<li class="file-stats">
<a href="#7732fe80266a12c4574ac3e07e91defe3b2e2c80">
src/fastq_chars.h
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<a href="#efff97bf05f1c01ea9979e2b749894a3926eb1b8">
src/fastq_join.cc
</a>
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<a href="#6f6e139f17b24056f909b0ad0837bde7fcc25d4c">
src/fastq_join.h
</a>
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<li class="file-stats">
<a href="#2791d358926c61f032472b3c3e0d11d7b665df7c">
src/mergepairs.cc
→
src/fastq_mergepairs.cc
</a>
</li>
<li class="file-stats">
<a href="#69f7b79d8cb3abc90660a8aebb7c2c289e6e6dc6">
src/mergepairs.h
→
src/fastq_mergepairs.h
</a>
</li>
<li class="file-stats">
<a href="#041870651e3cab1accf4fdb62a8c810a9800b1a7">
<span class="new-file">
+
src/fastq_stats.cc
</span>
</a>
</li>
<li class="file-stats">
<a href="#476e1b5b6f0db5da2515370a7294dbf0281c4db4">
src/utils/seqcmp.h
→
src/fastq_stats.h
</a>
</li>
<li class="file-stats">
<a href="#6f963d02896322eab19500836bca3f9a22619a35">
src/fastqops.cc
</a>
</li>
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<a href="#2d78b39ae6384856f7390467802408d407d20123">
src/fastqops.h
</a>
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<li class="file-stats">
<a href="#66934cf2fb3d65e60500632c125c6324b6bebbec">
src/fastx.cc
</a>
</li>
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<a href="#10eff3279cfc990f0a974eabcc8aa2d695e029f5">
src/fastx.h
</a>
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src/filter.cc
</a>
</li>
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<a href="#6cf66911c6f33458585d79abb14f14851f9fcb3f">
src/filter.h
</a>
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<a href="#f8033b5b738e4f851faa382f3ee8786c9fbd889d">
src/getseq.cc
</a>
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<a href="#08dd0514f803e877ea4de9eea3fbe6b40f348036">
src/getseq.h
</a>
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src/kmerhash.cc
</a>
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<a href="#c40c630cfc54837f37b946fe0e7213811d99d499">
src/kmerhash.h
</a>
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src/linmemalign.cc
</a>
</li>
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src/linmemalign.h
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src/maps.cc
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</a>
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src/mask.cc
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src/mask.h
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src/md5.c
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src/minheap.cc
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src/minheap.h
</a>
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src/msa.cc
</a>
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src/msa.h
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src/orient.cc
</a>
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src/orient.h
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src/otutable.cc
</a>
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src/otutable.h
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<a href="#369e8ccd4ce6ce2254c68ea46cedd3274d227209">
src/rereplicate.cc
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src/rereplicate.h
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src/results.cc
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src/results.h
</a>
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src/search.cc
</a>
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src/search.h
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</li>
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src/search_exact.cc
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src/search_exact.h
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src/searchcore.cc
</a>
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src/searchcore.h
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src/sff_convert.cc
</a>
</li>
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<a href="#c33f375cf554017a88aac7d1a9fc7ef4a92bb9db">
src/sff_convert.h
</a>
</li>
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<a href="#51af95f1e61ee7597aa42d06515abfacd20f6be7">
src/showalign.cc
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</li>
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src/showalign.h
</a>
</li>
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src/shuffle.cc
</a>
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src/shuffle.h
</a>
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src/sintax.cc
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</li>
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src/sintax.h
</a>
</li>
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src/sortbylength.cc
</a>
</li>
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src/sortbylength.h
</a>
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src/sortbysize.cc
</a>
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src/sortbysize.h
</a>
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src/subsample.cc
</a>
</li>
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src/subsample.h
</a>
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src/tax.cc
</a>
</li>
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src/tax.h
</a>
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src/udb.cc
</a>
</li>
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<a href="#b07e2e369a0aaced4736def4467531823ba029a2">
src/udb.h
</a>
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src/unique.cc
</a>
</li>
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<a href="#66c9effe8cface6705b21d65b07af421ab5d9487">
src/unique.h
</a>
</li>
<li class="file-stats">
<a href="#a7f9197a232a5a7ea53c78e84c4640821c00ca15">
src/userfields.cc
</a>
</li>
<li class="file-stats">
<a href="#2651f8c6e051ad6498b3c24ea077111b50eaafb7">
src/userfields.h
</a>
</li>
<li class="file-stats">
<a href="#fd94926041af2ce9c277ace5943e60e100bea483">
src/util.cc
</a>
</li>
<li class="file-stats">
<a href="#5f65ec0c183df81ed169516d4ec6c5508122dccd">
src/util.h
</a>
</li>
<li class="file-stats">
<a href="#18cf08ede5f357e754541448a0fbb8264876d1b1">
src/maps.h
→
src/utils/check_output_filehandle.cpp
</a>
</li>
<li class="file-stats">
<a href="#f150a6ed4631a1d26f19049cac142261f9660d47">
<span class="new-file">
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src/utils/check_output_filehandle.hpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#28fcf387230a31d802ff75d3e0421e23e7cb794d">
<span class="new-file">
+
src/utils/cigar.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#d772ef5a3b32caf6db63912c4ce5b440abe8703b">
src/utils/seqcmp.cc
→
src/utils/cigar.hpp
</a>
</li>
<li class="file-stats">
<a href="#73fa4467ec70ab1c13dd7d68da70e69f5d352b6e">
<span class="new-file">
+
src/utils/cigar_operations.hpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#dbc32425cf5ae73eac10084daa81be05ffa46508">
<span class="new-file">
+
src/utils/compare_strings_nocase.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#51780fbdff08bd7672518739fa209435ff12b57f">
<span class="new-file">
+
src/utils/compare_strings_nocase.hpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#81f8c01f7cd1993f334bd5d21c097e3c2a7d3d83">
<span class="new-file">
+
src/utils/fatal.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#be0d7e426f6bf73fb41537031ed8e91563d59711">
<span class="new-file">
+
src/utils/fatal.hpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#bded6e21361ddb0da070221fb40166f57d500817">
<span class="new-file">
+
src/utils/kmer_hash_struct.hpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#96309c954c4414b8eeeec5ccf5b68c570932e654">
src/utils/maps.cpp
</a>
</li>
<li class="file-stats">
<a href="#67c2c4aee6b0a8974ca4bfdb193025c844dcca71">
src/utils/maps.hpp
</a>
</li>
<li class="file-stats">
<a href="#24bcae30f08b22f9af3f5c3a123fae3616b92506">
<span class="new-file">
+
src/utils/open_file.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#ee7d8a478b58d5ce2bd32408218e34a60a14084b">
<span class="new-file">
+
src/utils/open_file.hpp
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</a>
</li>
<li class="file-stats">
<a href="#fc0fcef502db7dfc5b78368bbabd67239ea2aed4">
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+
src/utils/os_byteswap.cpp
</span>
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</li>
<li class="file-stats">
<a href="#3338378af5a153d5c3d1a59a9f37b826045287c8">
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src/utils/os_byteswap.hpp
</span>
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</li>
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<a href="#1da42c919b0b8e3b7d6e439c8d1e34a366a4e46c">
<span class="new-file">
+
src/utils/progress.hpp
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<li class="file-stats">
<a href="#6279caddcdc41837639a2f91bc8e4d4e09c68493">
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+
src/utils/seqcmp.cpp
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<a href="#23bc011d195d1bf693b9b5af3986c9e274879b1d">
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+
src/utils/seqcmp.hpp
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</li>
<li class="file-stats">
<a href="#d41e29ea10616b08a9bcfe59053acab04572d570">
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+
src/utils/span.hpp
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<li class="file-stats">
<a href="#2c297e29bc840b11172b252f06826c088a5fd704">
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src/utils/taxonomic_fields.h
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</li>
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<a href="#6d5940b2143dc5e4ba3ae4adf5bd238a46be601f">
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src/utils/xpthread.cpp
</span>
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</li>
<li class="file-stats">
<a href="#d13c44cc700010961956491b04a1224fbdca271f">
<span class="new-file">
+
src/utils/xpthread.hpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#b0109d980457466d1deec0f79c45e2b54114fdd5">
src/vsearch.cc
</a>
</li>
<li class="file-stats">
<a href="#d5c50f833cab4828d6d2b3f54dda35a42237db09">
src/vsearch.h
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</li>
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<a href="#dd779a506c83e7beac5573503ba0f5b7c7592b04">
src/xstring.h
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</ul>
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<div class="footer" style="margin-top: 10px;">
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