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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/mmseqs2">Debian Med / mmseqs2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/df23200b93c3e466d0c808857c0e08f81e6a0b3a">df23200b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-09-02T12:23:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build-depend on libsimde-dev 0.6.0-2 to get i386 patches from upstream
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/b09322a0cbb702dc19c760b5c9393fd1c9e79265">b09322a0</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-09-02T12:51:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix for i386
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/21e5e1fcccf3ed69f0c6408a4731c4cdc9a01960">21e5e1fc</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-09-02T13:16:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/patches/spelling: fix typos
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/152199318dfc4bcac188bb81696b4b786ee53bf6">15219931</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-09-02T13:16:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">typo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/6f59a6b879afe8071973c7f3667dba253888dfa7">6f59a6b8</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-09-02T13:17:25+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">release 12-113e3+ds-1
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<h4>6 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="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#2cd28d22eca59c0013ae61ced8c53c057572bb0f">
<span class="new-file">
+
debian/patches/simde_tweak
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<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
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+
debian/patches/spelling
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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/mmseqs2/-/compare/7927390603351bc43634d32e1a36e594db33b510...6f59a6b879afe8071973c7f3667dba253888dfa7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">mmseqs2 (12-113e3+ds-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mmseqs2 (12-113e3+ds-1) <span class="idiff left right">unstable</span>; 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"> * New upstream version</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Freshen debian/copyright</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * debian/rules: Ensure all for-loops fail if there is an error</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> * i386 build currently broken due to https://github.com/simd-everywhere/simde/issues/607</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Build-depend on libsimde-dev 0.6.0-2 to get i386 patches from upstream</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * debian/patches/spelling: fix typos</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> <span class="idiff left right">Tue, 01 Sep 2020 14:39:0</span>2 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> <span class="idiff left right">Wed, 02 Sep 2020 13:17:1</span>2 +0200</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">mmseqs2 (11-e1a1c+ds-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/7927390603351bc43634d32e1a36e594db33b510...6f59a6b879afe8071973c7f3667dba253888dfa7#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -9,7 +9,7 @@ Build-Depends-Arch: cmake,</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libzstd-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libbz2-dev,</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> libsimde-dev</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> libsimde-dev<span class="idiff left right"> (>= 0.6.0-2)</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/mmseqs2</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/mmseqs2.git</span>
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<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/7927390603351bc43634d32e1a36e594db33b510...6f59a6b879afe8071973c7f3667dba253888dfa7#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">spelling</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">simde_tweak</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">fix_tests.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">fix_util_installation.patch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">use_system_zstd.patch</span>
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<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/7927390603351bc43634d32e1a36e594db33b510...6f59a6b879afe8071973c7f3667dba253888dfa7#2cd28d22eca59c0013ae61ced8c53c057572bb0f"><strong>debian/patches/simde_tweak</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: work around SIMDe NATIVE_ALIASES issue</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</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;">--- mmseqs2.orig/src/commons/Util.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/commons/Util.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -597,41 +597,42 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> // Compute reverse complement of k-mer in 2-bit-per-nucleotide encoding (A: 00, C: 01, T: 10, G: 11)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> uint64_t Util::revComplement(const uint64_t kmer, const int k) {</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;">+</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> // broadcast 64bit to 128 bit</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __m128i x = _mm_cvtsi64_si128(kmer);</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __m128i x_up = _mm_cvtsi64_si128(kmer >> (uint64_t)4); // shift right by 2 nucleotides</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ simde__m128i x = simde_mm_cvtsi64_si128(kmer);</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ simde__m128i x_up = simde_mm_cvtsi64_si128(kmer >> (uint64_t)4); // shift right by 2 nucleotides</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> // create lookup (set 16 bytes in 128 bit)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> // a lookup entry at the index of two nucleotides (4 bit) describes the reverse</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> // complement of these two nucleotide in the higher 4 bits (lookup1) or in the lower 4 bits (lookup2)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> #define c (signed char)</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;">- __m128i lookup1 = _mm_set_epi8(c(0x50),c(0x10),c(0xD0),c(0x90),c(0x40),c(0x00),c(0xC0),c(0x80),</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ simde__m128i lookup1 = simde_mm_set_epi8(c(0x50),c(0x10),c(0xD0),c(0x90),c(0x40),c(0x00),c(0xC0),c(0x80),</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> c(0x70),c(0x30),c(0xF0),c(0xB0),c(0x60),c(0x20),c(0xE0),c(0xA0));</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;">- __m128i lookup2 = _mm_set_epi8(c(0x05),c(0x01),c(0x0D),c(0x09),c(0x04),c(0x00),c(0x0C),c(0x08),</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;">+ simde__m128i lookup2 = simde_mm_set_epi8(c(0x05),c(0x01),c(0x0D),c(0x09),c(0x04),c(0x00),c(0x0C),c(0x08),</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> c(0x07),c(0x03),c(0x0F),c(0x0B),c(0x06),c(0x02),c(0x0E),c(0x0A));</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> // set upper 8 bytes to 0 and revert order of lower 8 bytes</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __m128i upper = _mm_set_epi8(c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),</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;">+ simde__m128i upper = simde_mm_set_epi8(c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> 0,1,2,3,4,5,6,7);</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // _mm_set1_epi8: create 128 bit with all bytes set to given value</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // simde_mm_set1_epi8: create 128 bit with all bytes set to given value</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> // here: 0x0F (00001111) and 0xF0 (11110000)</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // _mm_and_si128: bitwise AND</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __m128i kmer1 = _mm_and_si128(x, _mm_set1_epi8(c(0x0F))); // get lower 4 bits</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __m128i kmer2 = _mm_and_si128(x_up, _mm_set1_epi8(c(0x0F))); // get higher 4 bits</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // simde_mm_and_si128: bitwise AND</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ simde__m128i kmer1 = simde_mm_and_si128(x, simde_mm_set1_epi8(c(0x0F))); // get lower 4 bits</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ simde__m128i kmer2 = simde_mm_and_si128(x_up, simde_mm_set1_epi8(c(0x0F))); // get higher 4 bits</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> #undef c</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // use _mm_shuffle_epi8 to look up reverse complement</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- kmer1 = _mm_shuffle_epi8(lookup1, kmer1);</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- kmer2 = _mm_shuffle_epi8(lookup2, kmer2);</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // use simde_mm_shuffle_epi8 to look up reverse complement</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ kmer1 = simde_mm_shuffle_epi8(lookup1, kmer1);</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ kmer2 = simde_mm_shuffle_epi8(lookup2, kmer2);</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // _mm_or_si128: bitwise OR</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- x = _mm_or_si128(kmer1, kmer2);</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // simde_mm_or_si128: bitwise OR</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ x = simde_mm_or_si128(kmer1, kmer2);</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> // set upper 8 bytes to 0 and revert order of lower 8 bytes</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- x = _mm_shuffle_epi8(x, upper);</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ x = simde_mm_shuffle_epi8(x, upper);</span></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="LC58" class="line" lang="diff"> // shift out the unused nucleotide positions (1 <= k <=32 )</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> // broadcast 128 bit to 64 bit</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return (((uint64_t)_mm_cvtsi128_si64(x)) >> (uint64_t)(64-2*k));</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return (((uint64_t)simde_mm_cvtsi128_si64(x)) >> (uint64_t)(64-2*k));</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/7927390603351bc43634d32e1a36e594db33b510...6f59a6b879afe8071973c7f3667dba253888dfa7#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Spelling typos fixes</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/data/workflow/searchslicedtargetprofile.sh</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/data/workflow/searchslicedtargetprofile.sh</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -69,7 +69,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> # predict NUM_SEQS_THAT_SATURATE as the average number of prefilter results per profile in previous steps</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # this allows to increase NUM_PROFS_IN_STEP</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;">+ # this allows one to increase NUM_PROFS_IN_STEP</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> if [ "${NUM_PREF_RESULTS_IN_ALL_PREV_STEPS}" -gt 0 ]; then</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> # BE MORE CAUTIOUS?</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> NUM_PROFS_PROCESSED="$((FIRST_INDEX_LINE-1))"</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/MMseqsBase.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/MMseqsBase.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -717,7 +717,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> {"DB", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::allDb },</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> {"DB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::VARIADIC, &DbValidator::allDb }}},</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> {"subtractdbs", subtractdbs, &par.subtractdbs, COMMAND_SET,</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;">- "Remove all entries from first DB occuring in second DB by key",</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "Remove all entries from first DB occurring in second DB by key",</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> NULL,</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> "Martin Steinegger <martin.steinegger@snu.ac.kr>",</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> "<i:resultDBLeft> <i:resultDBRight> <o:resultDB>",</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/commons/DBReader.cpp</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;">+++ mmseqs2/src/commons/DBReader.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -1106,7 +1106,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> if (idx != std::string::npos) {</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> ext = names[i].substr(idx);</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Debug(Debug::ERROR) << "File extention was not found but it is expected to be there!\n"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Debug(Debug::ERROR) << "File extension was not found but it is expected to be there!\n"</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> << "Filename: " << names[i] << ".\n";</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> EXIT(EXIT_FAILURE);</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/commons/Parameters.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/commons/Parameters.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -87,7 +87,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> PARAM_FORMAT_OUTPUT(PARAM_FORMAT_OUTPUT_ID, "--format-output", "Format alignment output", "Choose comma separated list of output columns from: query,target,evalue,gapopen,pident,fident,nident,qstart,qend,qlen\ntstart,tend,tlen,alnlen,raw,bits,cigar,qseq,tseq,qheader,theader,qaln,taln,qframe,tframe,mismatch,qcov,tcov\nqset,qsetid,tset,tsetid,taxid,taxname,taxlineage,qorfstart,qorfend,torfstart,torfend", typeid(std::string), (void *) &outfmt, ""),</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> PARAM_DB_OUTPUT(PARAM_DB_OUTPUT_ID, "--db-output", "Database output", "Return a result DB instead of a text file", typeid(bool), (void *) &dbOut, "", MMseqsParameter::COMMAND_EXPERT),</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> // --include-only-extendablediagonal</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PARAM_RESCORE_MODE(PARAM_RESCORE_MODE_ID, "--rescore-mode", "Rescore mode", "Rescore diagonals with:\n0: Hamming distance\n1: local alignment (score only)\n2: local alignment\n3: global alignment\n4: longest alignment fullfilling window quality criterion", typeid(int), (void *) &rescoreMode, "^[0-4]{1}$"),</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PARAM_RESCORE_MODE(PARAM_RESCORE_MODE_ID, "--rescore-mode", "Rescore mode", "Rescore diagonals with:\n0: Hamming distance\n1: local alignment (score only)\n2: local alignment\n3: global alignment\n4: longest alignment fulfilling window quality criterion", typeid(int), (void *) &rescoreMode, "^[0-4]{1}$"),</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> PARAM_WRAPPED_SCORING(PARAM_WRAPPED_SCORING_ID, "--wrapped-scoring", "Allow wrapped scoring", "Double the (nucleotide) query sequence during the scoring process to allow wrapped diagonal scoring around end and start", typeid(bool), (void *) &wrappedScoring, "", MMseqsParameter::COMMAND_ALIGN | MMseqsParameter::COMMAND_EXPERT),</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> PARAM_FILTER_HITS(PARAM_FILTER_HITS_ID, "--filter-hits", "Remove hits by seq. id. and coverage", "Filter hits by seq.id. and coverage", typeid(bool), (void *) &filterHits, "", MMseqsParameter::COMMAND_EXPERT),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="46" 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="LC46" class="line" lang="diff"> PARAM_SORT_RESULTS(PARAM_SORT_RESULTS_ID, "--sort-results", "Sort results", "Sort results: 0: no sorting, 1: sort by E-value (Alignment) or seq.id. (Hamming)", typeid(int), (void *) &sortResults, "^[0-1]{1}$", MMseqsParameter::COMMAND_EXPERT),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="p">@@ -130,8 +130,8 @@</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> PARAM_KMER_PER_SEQ(PARAM_KMER_PER_SEQ_ID, "--kmer-per-seq", "k-mers per sequence", "k-mers per sequence", typeid(int), (void *) &kmersPerSequence, "^[1-9]{1}[0-9]*$", MMseqsParameter::COMMAND_CLUSTLINEAR),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="49" 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="LC49" class="line" lang="diff"> PARAM_KMER_PER_SEQ_SCALE(PARAM_KMER_PER_SEQ_SCALE_ID, "--kmer-per-seq-scale", "Scale k-mers per sequence", "Scale k-mer per sequence based on sequence length as kmer-per-seq val + scale x seqlen", typeid(MultiParam<float>), (void *) &kmersPerSequenceScale, "^0(\\.[0-9]+)?|1(\\.0+)?$", MMseqsParameter::COMMAND_CLUSTLINEAR),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="50" 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="LC50" class="line" lang="diff"> PARAM_INCLUDE_ONLY_EXTENDABLE(PARAM_INCLUDE_ONLY_EXTENDABLE_ID, "--include-only-extendable", "Include only extendable", "Include only extendable", typeid(bool), (void *) &includeOnlyExtendable, "", MMseqsParameter::COMMAND_CLUSTLINEAR),</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="51" 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="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PARAM_IGNORE_MULTI_KMER(PARAM_IGNORE_MULTI_KMER_ID, "--ignore-multi-kmer", "Skip repeating k-mers", "Skip k-mers occuring multiple times (>=2)", typeid(bool), (void *) &ignoreMultiKmer, "", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="52" 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="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PARAM_HASH_SHIFT(PARAM_HASH_SHIFT_ID, "--hash-shift", "Shift hash", "Shift k-mer hash initilization", typeid(int), (void *) &hashShift, "^[1-9]{1}[0-9]*$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="53" 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="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PARAM_IGNORE_MULTI_KMER(PARAM_IGNORE_MULTI_KMER_ID, "--ignore-multi-kmer", "Skip repeating k-mers", "Skip k-mers occurring multiple times (>=2)", typeid(bool), (void *) &ignoreMultiKmer, "", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="54" 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="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PARAM_HASH_SHIFT(PARAM_HASH_SHIFT_ID, "--hash-shift", "Shift hash", "Shift k-mer hash initialization", typeid(int), (void *) &hashShift, "^[1-9]{1}[0-9]*$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> PARAM_PICK_N_SIMILAR(PARAM_PICK_N_SIMILAR_ID, "--pick-n-sim-kmer", "Add N similar to search", "Add N similar k-mers to search", typeid(int), (void *) &pickNbest, "^[1-9]{1}[0-9]*$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="56" 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="LC56" class="line" lang="diff"> PARAM_ADJUST_KMER_LEN(PARAM_ADJUST_KMER_LEN_ID, "--adjust-kmer-len", "Adjust k-mer length", "Adjust k-mer length based on specificity (only for nucleotides)", typeid(bool), (void *) &adjustKmerLength, "", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="57" 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="LC57" class="line" lang="diff"> PARAM_RESULT_DIRECTION(PARAM_RESULT_DIRECTION_ID, "--result-direction", "Result direction", "result is 0: query, 1: target centric", typeid(int), (void *) &resultDirection, "^[0-1]{1}$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="58" 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="LC58" class="line" lang="diff"><span class="p">@@ -155,9 +155,9 @@</span></span>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="59" 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="LC59" class="line" lang="diff"> PARAM_CONTIG_START_MODE(PARAM_CONTIG_START_MODE_ID, "--contig-start-mode", "Contig start mode", "Contig start can be 0: incomplete, 1: complete, 2: both", typeid(int), (void *) &contigStartMode, "^[0-2]{1}"),</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="60" 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="LC60" class="line" lang="diff"> PARAM_CONTIG_END_MODE(PARAM_CONTIG_END_MODE_ID, "--contig-end-mode", "Contig end mode", "Contig end can be 0: incomplete, 1: complete, 2: both", typeid(int), (void *) &contigEndMode, "^[0-2]{1}"),</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="61" 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="LC61" class="line" lang="diff"> PARAM_ORF_START_MODE(PARAM_ORF_START_MODE_ID, "--orf-start-mode", "Orf start mode", "Orf fragment can be 0: from start to stop, 1: from any to stop, 2: from last encountered start to stop (no start in the middle)", typeid(int), (void *) &orfStartMode, "^[0-2]{1}"),</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="62" 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="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PARAM_ORF_FORWARD_FRAMES(PARAM_ORF_FORWARD_FRAMES_ID, "--forward-frames", "Forward frames", "Comma-seperated list of frames on the forward strand to be extracted", typeid(std::string), (void *) &forwardFrames, ""),</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="63" 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="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PARAM_ORF_REVERSE_FRAMES(PARAM_ORF_REVERSE_FRAMES_ID, "--reverse-frames", "Reverse frames", "Comma-seperated list of frames on the reverse strand to be extracted", typeid(std::string), (void *) &reverseFrames, ""),</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="64" 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="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PARAM_USE_ALL_TABLE_STARTS(PARAM_USE_ALL_TABLE_STARTS_ID, "--use-all-table-starts", "Use all table starts", "Use all alteratives for a start codon in the genetic table, if false - only ATG (AUG)", typeid(bool), (void *) &useAllTableStarts, ""),</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="65" 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="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PARAM_ORF_FORWARD_FRAMES(PARAM_ORF_FORWARD_FRAMES_ID, "--forward-frames", "Forward frames", "Comma-separated list of frames on the forward strand to be extracted", typeid(std::string), (void *) &forwardFrames, ""),</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PARAM_ORF_REVERSE_FRAMES(PARAM_ORF_REVERSE_FRAMES_ID, "--reverse-frames", "Reverse frames", "Comma-separated list of frames on the reverse strand to be extracted", typeid(std::string), (void *) &reverseFrames, ""),</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PARAM_USE_ALL_TABLE_STARTS(PARAM_USE_ALL_TABLE_STARTS_ID, "--use-all-table-starts", "Use all table starts", "Use all alternatives for a start codon in the genetic table, if false - only ATG (AUG)", typeid(bool), (void *) &useAllTableStarts, ""),</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> PARAM_TRANSLATE(PARAM_TRANSLATE_ID, "--translate", "Translate orf", "Translate ORF to amino acid", typeid(int), (void *) &translate, "^[0-1]{1}"),</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> PARAM_CREATE_LOOKUP(PARAM_CREATE_LOOKUP_ID, "--create-lookup", "Create lookup", "Create database lookup file (can be very large)", typeid(int), (void *) &createLookup, "^[0-1]{1}", MMseqsParameter::COMMAND_EXPERT),</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> // indexdb</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="p">@@ -233,7 +233,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> // filtertaxdb</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> PARAM_TAXON_LIST(PARAM_TAXON_LIST_ID, "--taxon-list", "Selected taxa", "Taxonomy ID, possibly multiple values separated by ','", typeid(std::string), (void *) &taxonList, ""),</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> // view</span>
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<td class="diff-line-num new new_line" data-linenumber="75" 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="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PARAM_ID_LIST(PARAM_ID_LIST_ID, "--id-list", "Selected entries with key", "Entries to be printed seperated by ','", typeid(std::string), (void *) &idList, ""),</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PARAM_ID_LIST(PARAM_ID_LIST_ID, "--id-list", "Selected entries with key", "Entries to be printed separated by ','", typeid(std::string), (void *) &idList, ""),</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> PARAM_IDX_ENTRY_TYPE(PARAM_IDX_ENTRY_TYPE_ID, "--idx-entry-type", "Index entry type", "0: sequence, 1: src sequence, 2: header, 3: src header", typeid(int), (void *) &idxEntryType, "^[0-3]{1}$"),</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> // lca and addtaxonomy</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> PARAM_PICK_ID_FROM(PARAM_PICK_ID_FROM_ID, "--pick-id-from", "Extract mode", "Query 1, Target 2", typeid(int), (void *) &pickIdFrom, "^[1-2]{1}$"),</span>
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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="p">@@ -247,9 +247,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> PARAM_REPORT_MODE(PARAM_REPORT_MODE_ID, "--report-mode", "Report mode", "Taxonomy report mode 0: Kraken 1: Krona", typeid(int), (void *) &reportMode, "^[0-1]{1}$"),</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> // createtaxdb</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> PARAM_NCBI_TAX_DUMP(PARAM_NCBI_TAX_DUMP_ID, "--ncbi-tax-dump", "NCBI tax dump directory", "NCBI tax dump directory. The tax dump can be downloaded here \"ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\"", typeid(std::string), (void *) &ncbiTaxDump, ""),</span>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PARAM_TAX_MAPPING_FILE(PARAM_TAX_MAPPING_FILE_ID, "--tax-mapping-file", "Taxonomical mapping file", "File to map sequence identifer to taxonomical identifier", typeid(std::string), (void *) &taxMappingFile, ""),</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PARAM_TAX_MAPPING_FILE(PARAM_TAX_MAPPING_FILE_ID, "--tax-mapping-file", "Taxonomical mapping file", "File to map sequence identifier to taxonomical identifier", typeid(std::string), (void *) &taxMappingFile, ""),</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> // expandaln</span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PARAM_EXPANSION_MODE(PARAM_EXPANSION_MODE_ID, "--expansion-mode", "Expansion mode", "Update score, E-value, and sequence identity by 0: input alignment 1: rescoring the infered backtrace", typeid(int), (void *) &expansionMode, "^[0-2]{1}$"),</span></span>
</pre>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PARAM_EXPANSION_MODE(PARAM_EXPANSION_MODE_ID, "--expansion-mode", "Expansion mode", "Update score, E-value, and sequence identity by 0: input alignment 1: rescoring the inferred backtrace", typeid(int), (void *) &expansionMode, "^[0-2]{1}$"),</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> // taxonomy</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> PARAM_LCA_MODE(PARAM_LCA_MODE_ID, "--lca-mode", "LCA mode", "LCA Mode 1: Single Search LCA , 2: 2bLCA, 3: approx. 2bLCA, 4: top hit", typeid(int), (void *) &taxonomySearchMode, "^[1-4]{1}$"),</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> PARAM_TAX_OUTPUT_MODE(PARAM_TAX_OUTPUT_MODE_ID, "--tax-output-mode", "Taxonomy output mode", "0: output LCA, 1: output alignment 2: output both", typeid(int), (void *) &taxonomyOutpuMode, "^[0-2]{1}$"),</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/commons/ProfileStates.cpp</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/commons/ProfileStates.cpp</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="p">@@ -120,7 +120,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> if (nalph != 20)</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> {</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Debug(Debug::WARNING) << "Alphabet size of serialized context profile should be " << 20 << " but is acutally "<< nalph <<"!\n";</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Debug(Debug::WARNING) << "Alphabet size of serialized context profile should be " << 20 << " but is actually "<< nalph <<"!\n";</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> return -1;</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/taxonomy/aggregatetax.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/taxonomy/aggregatetax.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="p">@@ -227,7 +227,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> outDbStr = par.db5;</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> outDbIndexStr = par.db5Index;</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> } else if (par.voteMode == Parameters::AGG_TAX_MINUS_LOG_EVAL) {</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Debug(Debug::ERROR) << "voteMode is evalue-based but no alignment databse was provided. consider calling aggregatetaxweights\n";</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Debug(Debug::ERROR) << "voteMode is evalue-based but no alignment database was provided. consider calling aggregatetaxweights\n";</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> EXIT(EXIT_FAILURE);</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/7927390603351bc43634d32e1a36e594db33b510...6f59a6b879afe8071973c7f3667dba253888dfa7#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">@@ -23,12 +23,12 @@ i386_SIMD_LEVELS=sse2 sse</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">override_dh_auto_configure-arch:</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> $(foreach SIMD,$(AMD64_SIMD_LEVELS),export CXXFLAGS="$(CXXFLAGS) -m$(SIMD)" && export CFLAGS="$(CFLAGS) -m$(SIMD)" && \</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_$(SIMD) -- -DEXE_SUFFIX=-$(SIMD) -DVERSION_OVERRIDE=$(DEB_VERSION) -DNATIVE_ARCH=0<span class="idiff left right">; )</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_$(SIMD) -- -DEXE_SUFFIX=-$(SIMD) -DVERSION_OVERRIDE=$(DEB_VERSION) -DNATIVE_ARCH=0<span class="idiff left right"> && ) true</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> export CXXFLAGS="$(CXXFLAGS)" && export CFLAGS="$(CFLAGS)" && \</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_plain -- -DEXE_SUFFIX=-plain -DVERSION_OVERRIDE=$(DEB_VERSION) -DNATIVE_ARCH=0</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">ifeq (i386,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> $(foreach SIMD,$(i386_SIMD_LEVELS),export CXXFLAGS="$(CXXFLAGS) -m$(SIMD)" && export CFLAGS="$(CFLAGS) -m$(SIMD)" && \</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_$(SIMD) -- -DEXE_SUFFIX=-$(SIMD) -DVERSION_OVERRIDE=$(DEB_VERSION) -DNATIVE_ARCH=0<span class="idiff left right">; )</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_$(SIMD) -- -DEXE_SUFFIX=-$(SIMD) -DVERSION_OVERRIDE=$(DEB_VERSION) -DNATIVE_ARCH=0<span class="idiff left right"> && ) true</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> dh_auto_configure -- -DVERSION_OVERRIDE=$(DEB_VERSION)</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,9 +39,9 @@ override_dh_auto_configure-indep:</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">override_dh_auto_build-arch:</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> mkdir -p $(binprefix)</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> $(foreach SIMD,$(AMD64_SIMD_LEVELS),dh_auto_build --builddirectory build_$(SIMD)<span class="idiff left right">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> $(foreach SIMD,$(AMD64_SIMD_LEVELS),dh_auto_build --builddirectory build_$(SIMD)<span class="idiff left right"> && ) true</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">ifeq (i386,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> $(foreach SIMD,$(i386_SIMD_LEVELS),dh_auto_build --builddirectory build_$(SIMD)<span class="idiff left right">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> $(foreach SIMD,$(i386_SIMD_LEVELS),dh_auto_build --builddirectory build_$(SIMD)<span class="idiff left right"> && ) true</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> dh_auto_build</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -52,9 +52,9 @@ override_dh_auto_build-indep:</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">override_dh_auto_install-arch:</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> dh_install -pmmseqs2 debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> $(foreach SIMD,$(AMD64_SIMD_LEVELS),dh_auto_install --builddirectory build_$(SIMD) <span class="idiff left right">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> $(foreach SIMD,$(AMD64_SIMD_LEVELS),dh_auto_install --builddirectory build_$(SIMD) <span class="idiff left right">&& ) true</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">ifeq (i386,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> $(foreach SIMD,$(i386_SIMD_LEVELS),dh_auto_install --builddirectory build_$(SIMD) <span class="idiff left right">)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> $(foreach SIMD,$(i386_SIMD_LEVELS),dh_auto_install --builddirectory build_$(SIMD) <span class="idiff left right">&& ) true</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> dh_install -pmmseqs2 usr/bin/mmseqs-* usr/bin/</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> set -e && cd $(binprefix) \</span>
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