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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/e4e360cb252498ca8abcdb81a437ec882e7c5ceb">e4e360cb</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-20T22:59:55Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch to fix test_dbreaderzstd and include it in the unit test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/commit/46be5d63539b8a9f1ec1744ef9f38ec416f4837d">46be5d63</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-20T23:25:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch to fix test_indextable
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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>
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<h4>Changes:</h4>
<li id="5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">
<a href="https://salsa.debian.org/med-team/mmseqs2/compare/63dd49363845a0825a126935bfb0516e866dde9d...46be5d63539b8a9f1ec1744ef9f38ec416f4837d#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">@@ -6,8 +6,8 @@ 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 2019-07-2<span class="idiff left right">0 20:46:12.299793354</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 2019-07-2<span class="idiff left right">0 20:46:12.295793321</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 2019-07-2<span class="idiff left right">1 00:09:22.726611181</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 2019-07-2<span class="idiff left right">1 00:09:22.722611147</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,8 +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="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/test/TestBestAlphabet.cpp 2019-07-2<span class="idiff left right">0 20:46:12.299793354</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 2019-07-2<span class="idiff left right">0 20:46:12.295793321</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 2019-07-2<span class="idiff left right">1 00:09:22.726611181</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 2019-07-2<span class="idiff left right">1 00:09:22.722611147</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">@@ -50,8 +50,8 @@ Index: mmseqs2/src/test/TestBestAlphabet.cpp</td>
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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 2019-07-2<span class="idiff left right">0 20:46:12.299793354</span> +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 2019-07-2<span class="idiff left right">0 20:46:12.295793321</span> +0100</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 2019-07-2<span class="idiff left right">1 00:09:22.726611181</span> +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 2019-07-2<span class="idiff left right">1 00:09:22.722611147</span> +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="LC63" class="line" lang="diff"> aligner.ssw_init(query, tinySubMat, &subMat, subMat.alphabetSize, 2);</span>
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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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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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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 2019-07-2<span class="idiff left right">0 20:46:12.299793354</span> +0100</span></span>
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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 2019-07-2<span class="idiff left right">0 20:46:12.295793321</span> +0100</span></span>
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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 2019-07-2<span class="idiff left right">1 00:09:22.726611181</span> +0100</span></span>
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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 2019-07-2<span class="idiff left right">1 00:09:22.722611147</span> +0100</span></span>
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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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -94,8 +94,8 @@ Index: mmseqs2/src/test/TestDBReader.cpp</td>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="diff"> size_t id = reader3.getDbKey(i);</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="diff"><span class="gh" style="color: #999;">Index: mmseqs2/src/test/TestDBReaderIndexSerialization.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/test/TestDBReaderIndexSerialization.cpp 2019-07-2<span class="idiff left right">0 08:12:45.250499276</span> +0100</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/test/TestDBReaderIndexSerialization.cpp 2019-07-2<span class="idiff left right">0 20:47:05.360240870</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/test/TestDBReaderIndexSerialization.cpp 2019-07-2<span class="idiff left right">1 00:09:22.726611181</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/test/TestDBReaderIndexSerialization.cpp 2019-07-2<span class="idiff left right">1 00:09:22.722611147</span> +0100</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -4,7 +4,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="diff"> const char* binary_name = "test_dbreaderindexserialization";</span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="diff"> </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">@@ -105,3 +105,38 @@ Index: mmseqs2/src/test/TestDBReaderIndexSerialization.cpp</td>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="diff"> reader.open(DBReader<unsigned int>::NOSORT);</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="diff"> Debug(Debug::INFO) << reader.getSize() << " " << reader.getAminoAcidDBSize() << "\n";</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gh" style="color: #999;">Index: mmseqs2/src/test/TestDBReaderZstd.cpp</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/test/TestDBReaderZstd.cpp 2019-07-21 00:09:22.726611181 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/test/TestDBReaderZstd.cpp 2019-07-21 00:09:22.722611147 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -129,9 +129,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> "GCTATTATATCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCT"</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> "CGCATTTTTATGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCA";</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- writer.writeData((char*)data,strlen(data), 1,0);</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ writer.writeData((char*)data,strlen(data), 1, 0);</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> writer.close();</span>
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<pre style="margin: 0;">+<span id="LC119" 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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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::cout << "Before reader" << "\n";</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" 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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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::cout << "After reader" << "\n";</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> reader.open(0);</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> reader.readMmapedDataInMemory();</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> reader.printMagicNumber();</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gh" style="color: #999;">Index: mmseqs2/src/test/TestIndexTable.cpp</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/test/TestIndexTable.cpp 2019-07-20 22:31:34.645118021 +0100</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/test/TestIndexTable.cpp 2019-07-21 00:11:43.055794731 +0100</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -17,11 +17,7 @@</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> Parameters &par = Parameters::getInstance();</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> SubstitutionMatrix subMat(par.scoringMatrixFile.c_str(), 8.0, -0.2f);</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> DBReader<unsigned int> dbr(</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "/Users/mad/Documents/databases/db_small/db_small",</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// "/Users/mad/Documents/databases/mmseqs_benchmark/benchmarks/protein_search_uniscop/db/mmseqs/db_sw",</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "/Users/mad/Documents/databases/db_small/db_small.index"</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// "/Users/mad/Documents/databases/mmseqs_benchmark/benchmarks/protein_search_uniscop/db/mmseqs/db_sw.index"</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- , 1, 0);</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "../example-data/DB", "../example-data/DB.index", 1, 1);</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> dbr.open(DBReader<unsigned int>::LINEAR_ACCCESS);</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> </span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> Sequence *s = new Sequence(32000, Parameters::DBTYPE_AMINO_ACIDS, &subMat, 6, true, false);</span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/compare/63dd49363845a0825a126935bfb0516e866dde9d...46be5d63539b8a9f1ec1744ef9f38ec416f4837d#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">@@ -71,6 +71,8 @@ echo "Invoking test_dbreader"</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="shell">./test_dbreader</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Invoking test_dbreaderindexserialization"</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell">./test_dbreaderindexserialization</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Invoking test_dbreaderzstd"</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell">./test_dbreaderzstd</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC77" 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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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#echo "Invoke test_alignmentperformance"</span></span>
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