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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>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/commit/63dd49363845a0825a126935bfb0516e866dde9d">63dd4936</a></strong>
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<span>by Shayan Doust</span>
<i>at 2019-07-20T20:00:45Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch dbreaderserialization test and include in unit test
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">
debian/patches/fix_tests.patch
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">
<a href="https://salsa.debian.org/med-team/mmseqs2/commit/63dd49363845a0825a126935bfb0516e866dde9d#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 2019-07-20 <span class="idiff left right">19:59:12.396009495</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 <span class="idiff left right">19:59:12.388009427</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 <span class="idiff left right">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 2019-07-20 <span class="idiff left right">20:46:12.295793321</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 2019-07-20 <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 <span class="idiff left right">19:59:12.39200946</span>1 +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">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 2019-07-20 <span class="idiff left right">20:46:12.29579332</span>1 +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 2019-07-20 <span class="idiff left right">19:59:12.396009495</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 2019-07-20 <span class="idiff left right">19:59:12.39200946</span>1 +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 2019-07-20 <span class="idiff left right">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 2019-07-20 <span class="idiff left right">20:46:12.29579332</span>1 +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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -63,8 +63,8 @@ Index: mmseqs2/src/test/TestAlignmentPerformance.cpp</td>
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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 2019-07-20 <span class="idiff left right">08:12:45.250499276</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 2019-07-20 20:<span class="idiff left right">00:32.384684139</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 2019-07-20 <span class="idiff left right">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 2019-07-20 20:<span class="idiff left right">46:12.295793321</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">@@ -92,3 +92,16 @@ Index: mmseqs2/src/test/TestDBReader.cpp</td>
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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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<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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94
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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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95
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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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96
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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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97
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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 2019-07-20 08:12:45.250499276 +0100</span></span>
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98
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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 2019-07-20 20:47:05.360240870 +0100</span></span>
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99
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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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100
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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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101
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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"> int main (int, const char**) {</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DBReader<unsigned int> reader("", "/Users/mirdita/tmp/db.index", 1, DBReader<unsigned int>::USE_INDEX);</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DBReader<unsigned int> reader("", "../example-data/DB.index", 1, DBReader<unsigned int>::USE_INDEX);</span></span>
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105
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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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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> </span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> Debug(Debug::INFO) << reader.getSize() << " " << reader.getAminoAcidDBSize() << "\n";</span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/commit/63dd49363845a0825a126935bfb0516e866dde9d#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">@@ -69,6 +69,8 @@ echo "Invoking test_bestalphabet"</td>
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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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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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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 class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Invoking test_dbreaderindexserialization"</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell">./test_dbreaderindexserialization</span>
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72
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"></span>
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73
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<pre style="margin: 0;"> <span id="LC75" 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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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#echo "Invoke test_alignmentperformance"</span></span>
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