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<h3>
Shayan Doust 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/a5b18b086a82bff7c362970db2fadaf1b58ba6dc">a5b18b08</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-20T18:45:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch to fix test_alignmentperformance
I have excluded this as it takes a *very* long time to perform and probably isn't worth it. Probably should be used alongside a profiler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/commit/72d91fc09d93cb8fde052ba1bb0e5bc69e9c54a5">72d91fc0</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-20T19:16:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch test_dbreader and include this in the unit test
</pre>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">
debian/patches/fix_tests.patch
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">
<a href="https://salsa.debian.org/med-team/mmseqs2/compare/968f4d6ec81844e7d448281bfed3a52b3b01fba1...72d91fc09d93cb8fde052ba1bb0e5bc69e9c54a5#5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70"><strong>debian/patches/fix_tests.patch</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">@@ -6,17 +6,16 @@ Last-Update: 2019-07-20</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></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;">--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 1<span class="idiff left right">7:51:23.891331720</span> +0100</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;">+++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 1<span class="idiff left right">7:51:23.879331619</span> +0100</span></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;">--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 1<span class="idiff left right">9:59:12.396009495</span> +0100</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;">+++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 1<span class="idiff left right">9:59:12.388009427</span> +0100</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -18,10 +18,12 @@</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> ScoreMatrix* unserialized = ScoreMatrix::unserialize(serialized, subMat.alphabetSize, 3);</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"> Debug(Debug::INFO) << unserialized->elementSize << " " << unserialized->rowSize << " "</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- << unserialized->score[0] << " " << unserialized->index[0] << "\n";</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ScoreMatrix::cleanup(unserialized);</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ << unserialized->score[0] << "\n";</span></span>
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<pre style="margin: 0;">-<span id="LC19" 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="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ScoreMatrix::cleanup(unserialized);</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> free(serialized);</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;">- ScoreMatrix::cleanup(extMattwo);</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;">+ free(extMattwo);</span></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">@@ -27,8 +26,8 @@ Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gh" style="color: #999;">Index: mmseqs2/src/test/TestBestAlphabet.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/test/TestBestAlphabet.cpp 2019-07-20 <span class="idiff left right">08:12:45.250499276</span> +0100</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/test/TestBestAlphabet.cpp 2019-07-20 1<span class="idiff left right">7:52:58.384128682</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/test/TestBestAlphabet.cpp 2019-07-20 <span class="idiff left right">19:59:12.396009495</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/test/TestBestAlphabet.cpp 2019-07-20 1<span class="idiff left right">9:59:12.392009461</span> +0100</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -58,7 +58,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> ///////// | ////////////////</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> ///////// Choose substitution matrix here V ! ////////////////</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">@@ -49,3 +48,47 @@ Index: mmseqs2/src/test/TestBestAlphabet.cpp</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> DBReader<unsigned int> seqDb(dbPath.c_str(), dbIndexPath.c_str(), 1, DBReader<unsigned int>::USE_DATA|DBReader<unsigned int>::USE_INDEX);</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> seqDb.open(DBReader<unsigned int>::NOSORT);</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gh" style="color: #999;">Index: mmseqs2/src/test/TestAlignmentPerformance.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/test/TestAlignmentPerformance.cpp 2019-07-20 19:59:12.396009495 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/test/TestAlignmentPerformance.cpp 2019-07-20 19:59:12.392009461 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -83,7 +83,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> int gap_extend = 1;</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> int mode = 0;</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> size_t cells = 0;</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- std::vector<std::string> sequences = readData("/Users/mad/Documents/databases/rfam/Rfam.fasta");</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::vector<std::string> sequences = readData("../example-data/DB.fasta");</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> for(size_t seq_i = 0; seq_i < sequences.size(); seq_i++){</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> query->mapSequence(1,1,sequences[seq_i].c_str());</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> aligner.ssw_init(query, tinySubMat, &subMat, subMat.alphabetSize, 2);</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gh" style="color: #999;">Index: mmseqs2/src/test/TestDBReader.cpp</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</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;">--- mmseqs2.orig/src/test/TestDBReader.cpp 2019-07-20 08:12:45.250499276 +0100</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;">+++ mmseqs2/src/test/TestDBReader.cpp 2019-07-20 20:00:32.384684139 +0100</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -14,7 +14,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> int main (int, const char**) {</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> // DBReader test</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DBReader<unsigned int> reader("dataLinear", "dataLinear.index", 1, 0);</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DBReader<unsigned int> reader("dataLinear", "dataLinear.index", 1, 1);</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> reader.open(0);</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> reader.readMmapedDataInMemory();</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> reader.printMagicNumber();</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -24,7 +24,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> std::cout << reader.getData(i, 0) << std::endl;</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> reader.close();</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DBReader<unsigned int> reader2("dataGap", "dataGap.index", 1, 0);</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DBReader<unsigned int> reader2("dataGap", "dataGap.index", 1, 1);</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> reader2.open(0);</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> std::cout << reader2.getSize() << std::endl;</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> for(size_t i = 0; i < reader2.getSize(); i++){</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -45,7 +45,7 @@</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> std::cout << "Check length: " << (reader2.getSeqLens(reader2.getId(12)) == 10) << std::endl;</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> reader2.close();</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> // test sort mode</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DBReader<unsigned int> reader3("dataGap", "dataGap.index", 1, 0);</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DBReader<unsigned int> reader3("dataGap", "dataGap.index", 1, 1);</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> reader3.open(DBReader<unsigned int>::SORT_BY_LENGTH);</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> for(size_t i = 0; i < reader3.getSize(); i++){</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> size_t id = reader3.getDbKey(i);</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/mmseqs2/compare/968f4d6ec81844e7d448281bfed3a52b3b01fba1...72d91fc09d93cb8fde052ba1bb0e5bc69e9c54a5#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -67,3 +67,9 @@ echo "Invoking test_scorematrixserialization"</td>
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67
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="shell">./test_scorematrixserialization</span>
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68
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Invoking test_bestalphabet"</span></span>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell">./test_bestalphabet</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Invoking test_dbreader"</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell">./test_dbreader</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Takes a very long time to complete</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#echo "Invoke test_alignmentperformance"</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#./test_alignmentperformance</span></span></pre>
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